diff --git a/DESCRIPTION b/DESCRIPTION
index f572c254..c2f88768 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: hubValidations
 Title: Testing framework for hubverse hub validations
-Version: 0.0.0.9005
+Version: 0.0.0.9006
 Authors@R: c(
     person(
         given = "Anna", 
diff --git a/NEWS.md b/NEWS.md
index 1404f2ca..7ba8f506 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# hubValidations 0.0.0.9006
+
+* `validate_pr()` now checks for deletions of previously submitted model metadata files and modifications or deletions of previously submitted model output files, adding an `<error/check_error>` class object to the function output for each detected modified/deleted file (#43 & #44).
+
 # hubValidations 0.0.0.9005
 
 * Improved handling of numeric output type IDs (including high precision floating points / values with trailing zeros), especially when overall hub output type ID column is character. This previously lead to a number of bugs and false validation failures (#58 & #54) which are addressed in this version.
diff --git a/R/validate_pr.R b/R/validate_pr.R
index 79c70dec..be28894e 100644
--- a/R/validate_pr.R
+++ b/R/validate_pr.R
@@ -41,15 +41,39 @@ validate_pr <- function(hub_path = ".", gh_repo, pr_number,
         gh_repo = gh_repo,
         pr_number = pr_number
       )
-      pr_filenames <- purrr::map_chr(pr_files, ~ .x$filename)
-      model_output_files <- get_pr_dir_files(
-        pr_filenames,
-        model_output_dir
-      )
-      model_metadata_files <- get_pr_dir_files(
-        pr_filenames,
-        model_metadata_dir
-      )
+      pr_df <- tibble::tibble(
+        filename = purrr::map_chr(pr_files, ~ .x$filename),
+        status = purrr::map_chr(pr_files, ~ .x$status),
+        model_output = purrr::map_lgl(
+          .data$filename,
+          ~ fs::path_has_parent(.x, model_output_dir) &&
+            stringr::str_detect(.x, "README", negate = TRUE)
+        ),
+        model_metadata = purrr::map_lgl(
+          .data$filename,
+          ~ fs::path_has_parent(.x, model_metadata_dir) &&
+            stringr::str_detect(.x, "README", negate = TRUE)
+        ),
+      ) %>%
+        dplyr::mutate(
+          rel_path = dplyr::case_when(
+            .data$model_output ~ fs::path_rel(.data$filename, model_output_dir),
+            .data$model_metadata ~ fs::path_rel(.data$filename, model_metadata_dir),
+            .default = .data$filename
+          )
+        )
+      inform_unvalidated_files(pr_df)
+
+      model_output_files <- pr_df$rel_path[pr_df$model_output &
+        pr_df$status != "removed"]
+      model_metadata_files <- pr_df$rel_path[pr_df$model_metadata &
+        pr_df$status != "removed"]
+
+      file_modifications <- purrr::map(
+        c("model_output", "model_metadata"),
+        ~ check_pr_modf_del_files(pr_df, file_type = .x)
+      ) %>%
+        purrr::reduce(combine)
 
       model_output_vals <- purrr::map(
         model_output_files,
@@ -75,8 +99,10 @@ validate_pr <- function(hub_path = ".", gh_repo, pr_number,
         purrr::list_flatten() %>%
         as_hub_validations()
 
+
       validations <- combine(
         validations,
+        file_modifications,
         model_output_vals,
         model_metadata_vals
       )
@@ -96,39 +122,15 @@ validate_pr <- function(hub_path = ".", gh_repo, pr_number,
       )
     }
   )
-
-  inform_unvalidated_files(
-    model_output_files,
-    model_metadata_files,
-    pr_filenames
-  )
   return(validations)
 }
 
-get_pr_dir_files <- function(pr_filenames, dir_name) {
-  pr_filenames[
-    fs::path_has_parent(pr_filenames, dir_name)
-  ] %>%
-    stringr::str_subset("README", negate = TRUE) %>%
-    fs::path_rel(dir_name)
-}
-
-inform_unvalidated_files <- function(model_output_files,
-                                     model_metadata_files,
-                                     pr_filenames) {
-  validated_files <- c(model_output_files, model_metadata_files)
-  if (length(pr_filenames) == length(validated_files)) {
+# Sends message reporting any files with changes in PR that were not validated.
+inform_unvalidated_files <- function(pr_df) {
+  unvalidated_files <- pr_df[!pr_df$model_output & !pr_df$model_metadata, "filename", drop = TRUE]
+  if (length(unvalidated_files) == 0L) {
     return(invisible(NULL))
   }
-  if (length(validated_files) == 0L) {
-    unvalidated_files <- pr_filenames
-  } else {
-    validated_idx <- purrr::map_int(
-      validated_files,
-      ~ grep(.x, pr_filenames, fixed = TRUE)
-    )
-    unvalidated_files <- pr_filenames[-validated_idx]
-  }
 
   unvalidated_bullets <- purrr::map_chr(
     unvalidated_files,
@@ -143,3 +145,37 @@ inform_unvalidated_files <- function(model_output_files,
     )
   )
 }
+# Checks for model output file modifications and model output & model metadata
+# file deletions. Returns an <error/check_error>⁠ condition class object if any
+# modification or deletion detected.
+check_pr_modf_del_files <- function(pr_df, file_type = c(
+                                      "model_output",
+                                      "model_metadata"
+                                    )) {
+  file_type <- rlang::arg_match(file_type)
+  df <- pr_df[pr_df[[file_type]], ]
+  df <- switch(file_type,
+    model_output = df[df$status %in% c("removed", "modified"), ],
+    model_metadata = df[df$status == "removed", ]
+  )
+
+  purrr::imap(
+    .x = df$rel_path,
+    ~ hubValidations::capture_check_cnd(
+      check = FALSE,
+      file_path = .x,
+      msg_subject = paste(
+        "Previously submitted",
+        stringr::str_replace(file_type, "_", " "),
+        "files"
+      ),
+      msg_verbs = c("were not", "must not be"),
+      msg_attribute = paste0(df$status[.y], "."),
+      details = cli::format_inline(
+        "{.path {df$filename[.y]}} {df$status[.y]}."
+      ),
+      error = TRUE
+    )
+  ) %>%
+    hubValidations::as_hub_validations()
+}
diff --git a/tests/testthat/_snaps/validate_pr.md b/tests/testthat/_snaps/validate_pr.md
index e81cbd87..15d76172 100644
--- a/tests/testthat/_snaps/validate_pr.md
+++ b/tests/testthat/_snaps/validate_pr.md
@@ -211,3 +211,195 @@
         ..$ use_cli_format: logi TRUE
         ..- attr(*, "class")= chr [1:5] "check_error" "hub_check" "rlang_error" "error" ...
 
+# validate_pr flags modifications and deletions in PR
+
+    Code
+      str(checks)
+    Output
+      Classes 'hub_validations', 'list'  hidden list of 28
+       $ valid_config      :List of 4
+        ..$ message       : chr "All hub config files are valid. \n "
+        ..$ where         : chr "mod_del_hub"
+        ..$ call          : chr "check_config_hub_valid"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $                   :List of 6
+        ..$ message       : chr "Previously submitted model output files must not be modified. \n 'model-output/hub-baseline/2022-10-08-hub-base"| __truncated__
+        ..$ trace         : NULL
+        ..$ parent        : NULL
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ call          : chr ".f"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_error" "hub_check" "rlang_error" "error" ...
+       $                   :List of 6
+        ..$ message       : chr "Previously submitted model output files must not be removed. \n 'model-output/team1-goodmodel/2022-10-15-team1-"| __truncated__
+        ..$ trace         : NULL
+        ..$ parent        : NULL
+        ..$ where         : 'fs_path' chr "team1-goodmodel/2022-10-15-team1-goodmodel.csv"
+        ..$ call          : chr ".f"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_error" "hub_check" "rlang_error" "error" ...
+       $                   :List of 6
+        ..$ message       : chr "Previously submitted model metadata files must not be removed. \n 'model-metadata/team1-goodmodel.yaml' removed."
+        ..$ trace         : NULL
+        ..$ parent        : NULL
+        ..$ where         : 'fs_path' chr "team1-goodmodel.yaml"
+        ..$ call          : chr ".f"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_error" "hub_check" "rlang_error" "error" ...
+       $ file_exists       :List of 4
+        ..$ message       : chr "File exists at path 'model-output/hub-baseline/2022-10-08-hub-baseline.csv'. \n "
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ call          : chr "check_file_exists"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ file_name         :List of 4
+        ..$ message       : chr "File name \"2022-10-08-hub-baseline.csv\" is valid. \n "
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ call          : chr "check_file_name"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ file_location     :List of 4
+        ..$ message       : chr "File directory name matches `model_id`\n                                           metadata in file name. \n "
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ call          : chr "check_file_location"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ round_id_valid    :List of 4
+        ..$ message       : chr "`round_id` is valid. \n "
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ call          : chr "check_valid_round_id"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ file_format       :List of 4
+        ..$ message       : chr "File is accepted hub format. \n "
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ call          : chr "check_file_format"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ metadata_exists   :List of 4
+        ..$ message       : chr "Metadata file exists at path 'model-metadata/hub-baseline.yml'. \n "
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ call          : chr "check_submission_metadata_file_exists"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ file_read         :List of 4
+        ..$ message       : chr "File could be read successfully. \n "
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ call          : chr "check_file_read"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ valid_round_id_col:List of 4
+        ..$ message       : chr "`round_id_col` name is valid. \n "
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ call          : chr "check_valid_round_id_col"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ unique_round_id   :List of 4
+        ..$ message       : chr "`round_id` column \"origin_date\" contains a single, unique round ID value. \n "
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ call          : chr "check_tbl_unique_round_id"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ match_round_id    :List of 4
+        ..$ message       : chr "All `round_id_col` \"origin_date\" values match submission `round_id` from file name. \n "
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ call          : chr "check_tbl_match_round_id"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ colnames          :List of 4
+        ..$ message       : chr "Column names are consistent with expected round task IDs and std column names. \n "
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ call          : chr "check_tbl_colnames"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ col_types         :List of 4
+        ..$ message       : chr "Column data types match hub schema. \n "
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ call          : chr "check_tbl_col_types"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ valid_vals        :List of 5
+        ..$ message       : chr "`tbl` contains valid values/value combinations.  \n "
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ error_tbl     : NULL
+        ..$ call          : chr "check_tbl_values"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ rows_unique       :List of 4
+        ..$ message       : chr "All combinations of task ID column/`output_type`/`output_type_id` values are unique. \n "
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ call          : chr "check_tbl_rows_unique"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ req_vals          :List of 5
+        ..$ message       : chr "Required task ID/output type/output type ID combinations all present.  \n "
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ missing       : tibble [0 x 6] (S3: tbl_df/tbl/data.frame)
+        .. ..$ origin_date   : chr(0) 
+        .. ..$ target        : chr(0) 
+        .. ..$ horizon       : chr(0) 
+        .. ..$ location      : chr(0) 
+        .. ..$ output_type   : chr(0) 
+        .. ..$ output_type_id: chr(0) 
+        ..$ call          : chr "check_tbl_values_required"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ value_col_valid   :List of 4
+        ..$ message       : chr "Values in column `value` all valid with respect to modeling task config. \n "
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ call          : chr "check_tbl_value_col"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ value_col_non_desc:List of 5
+        ..$ message       : chr "Values in `value` column are non-decreasing as output_type_ids increase for all unique task ID\n    value/outpu"| __truncated__
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ error_tbl     : NULL
+        ..$ call          : chr "check_tbl_value_col_ascending"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ value_col_sum1    :List of 4
+        ..$ message       : chr "No pmf output types to check for sum of 1. Check skipped."
+        ..$ where         : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv"
+        ..$ call          : chr "check_tbl_value_col_sum1"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ...
+       $ file_exists       :List of 4
+        ..$ message       : chr "File exists at path 'model-output/team1-goodmodel/2022-10-22-team1-goodmodel.csv'. \n "
+        ..$ where         : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv"
+        ..$ call          : chr "check_file_exists"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ file_name         :List of 4
+        ..$ message       : chr "File name \"2022-10-22-team1-goodmodel.csv\" is valid. \n "
+        ..$ where         : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv"
+        ..$ call          : chr "check_file_name"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ file_location     :List of 4
+        ..$ message       : chr "File directory name matches `model_id`\n                                           metadata in file name. \n "
+        ..$ where         : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv"
+        ..$ call          : chr "check_file_location"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ round_id_valid    :List of 4
+        ..$ message       : chr "`round_id` is valid. \n "
+        ..$ where         : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv"
+        ..$ call          : chr "check_valid_round_id"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ file_format       :List of 4
+        ..$ message       : chr "File is accepted hub format. \n "
+        ..$ where         : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv"
+        ..$ call          : chr "check_file_format"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ...
+       $ metadata_exists   :List of 6
+        ..$ message       : chr "Metadata file does not exist at path 'model-metadata/team1-goodmodel.yml' or\n                                 "| __truncated__
+        ..$ trace         : NULL
+        ..$ parent        : NULL
+        ..$ where         : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv"
+        ..$ call          : chr "check_submission_metadata_file_exists"
+        ..$ use_cli_format: logi TRUE
+        ..- attr(*, "class")= chr [1:5] "check_error" "hub_check" "rlang_error" "error" ...
+
diff --git a/tests/testthat/test-validate_pr.R b/tests/testthat/test-validate_pr.R
index ddae6155..de2c59de 100644
--- a/tests/testthat/test-validate_pr.R
+++ b/tests/testthat/test-validate_pr.R
@@ -1,39 +1,72 @@
 test_that("validate_pr works on valid PR", {
-    skip_if_offline()
+  skip_if_offline()
 
-    temp_hub <- fs::path(tempdir(), "valid_sb_hub")
-    gert::git_clone(url = "https://github.com/Infectious-Disease-Modeling-Hubs/ci-testhub-simple",
-                    path = temp_hub,
-                    branch = "pr-valid")
+  temp_hub <- fs::path(tempdir(), "valid_sb_hub")
+  gert::git_clone(
+    url = "https://github.com/Infectious-Disease-Modeling-Hubs/ci-testhub-simple",
+    path = temp_hub,
+    branch = "pr-valid"
+  )
 
-   checks <- validate_pr(hub_path = temp_hub,
-                gh_repo = "Infectious-Disease-Modeling-Hubs/ci-testhub-simple",
-                pr_number = 4,
-                skip_submit_window_check = TRUE)
-
-   expect_snapshot(str(checks))
-   expect_invisible(suppressMessages(check_for_errors(checks)))
-   expect_message(check_for_errors(checks),
-                  regexp = "All validation checks have been successful.")
+  checks <- validate_pr(
+    hub_path = temp_hub,
+    gh_repo = "Infectious-Disease-Modeling-Hubs/ci-testhub-simple",
+    pr_number = 4,
+    skip_submit_window_check = TRUE
+  )
 
+  expect_snapshot(str(checks))
+  expect_invisible(suppressMessages(check_for_errors(checks)))
+  expect_message(check_for_errors(checks),
+    regexp = "All validation checks have been successful."
+  )
 })
 
 test_that("validate_pr works on invalid PR", {
-    skip_if_offline()
+  skip_if_offline()
+
+  temp_hub <- fs::path(tempdir(), "invalid_sb_hub")
+  gert::git_clone(
+    url = "https://github.com/Infectious-Disease-Modeling-Hubs/ci-testhub-simple",
+    path = temp_hub,
+    branch = "pr-missing-taskid"
+  )
+
+  checks <- validate_pr(
+    hub_path = temp_hub,
+    gh_repo = "Infectious-Disease-Modeling-Hubs/ci-testhub-simple",
+    pr_number = 5,
+    skip_submit_window_check = TRUE
+  )
 
-    temp_hub <- fs::path(tempdir(), "invalid_sb_hub")
-    gert::git_clone(url = "https://github.com/Infectious-Disease-Modeling-Hubs/ci-testhub-simple",
-                    path = temp_hub,
-                    branch = "pr-missing-taskid")
+  expect_snapshot(str(checks))
 
-    checks <- validate_pr(hub_path = temp_hub,
-                          gh_repo = "Infectious-Disease-Modeling-Hubs/ci-testhub-simple",
-                          pr_number = 5,
-                          skip_submit_window_check = TRUE)
+  expect_error(
+    suppressMessages(check_for_errors(checks))
+  )
+})
+
+test_that("validate_pr flags modifications and deletions in PR", {
+  skip_if_offline()
 
-    expect_snapshot(str(checks))
+  temp_hub <- fs::path(tempdir(), "mod_del_hub")
+  gert::git_clone(
+    url = "https://github.com/Infectious-Disease-Modeling-Hubs/ci-testhub-simple",
+    path = temp_hub,
+    branch = "test-mod-del"
+  )
 
-    expect_error(
-        suppressMessages(check_for_errors(checks))
+  checks <- suppressMessages(
+    validate_pr(
+      hub_path = temp_hub,
+      gh_repo = "Infectious-Disease-Modeling-Hubs/ci-testhub-simple",
+      pr_number = 6,
+      skip_submit_window_check = TRUE
     )
+  )
+
+  expect_snapshot(str(checks))
+  expect_error(
+    suppressMessages(check_for_errors(checks))
+  )
 })