Breakpoints are sometimes not properly recognized

[sewbacca]

I can't reproduce this bug in another project.
I'm using Love2D and wrap the update and draw calls arround a lldebugger.call, so that any breakpoints and whatever should get recognized. However recently in a project I noticed a strange and annoying behaviour.
Let's say I have main.lua, A.lua, B.lua, C.lua, and D.lua. The module D is used from A to C and in main.lua. Now I can easly create breakpoints in main.lua, A.lua and D.lua, but when trying to put breakpoints in B.lua or C.lua, the debugger steps right over them.
The only way that the debugger recognizes the breakpoints, is to step into B.lua or C.lua and put breakpoints when I am inside that file. Untill the end of this debugging session, any new breakpoints are recognized properly. If I restart the debugger, the same behaviour repeats.
I'm sorry, that I can't put an example to reproduce the behaviour, I had trouble finding a way. If I come up with an example, I will post it here.

Edit:
Interesting side effect: When copying the project files into another directory, there the issue disappears. Are there maybe any caches that are responsible?

Edit 2:
I could solve the issue by deleting the contents of %appdata%\Code\User\workspaceStorage

[tomblind]

Does this still occur, or did deleting %appdata%\Code\User\workspaceStorage solve the issue?

[sewbacca]

Does this still occur, or did deleting %appdata%\Code\User\workspaceStorage solve the issue?

It did happen, after I deleted it, again. However after the second time, it didn't occur again.