Two Ontology Files Being Updated Inconsistently after Merge

[giraygi]

Describe the bug
There started to appear two ontology files in download after a merge operation in our instance (https://service.tib.eu/wp4tib/). The second file does not have a name and its name is OntologyID(Anonymous-1234).owl. After that point, some changes in our project started to be reflected to both of the files while some changes only being reflected to the anonymous file. Plus, some annotations started to reappear or appear multiple times after removing them. And some annotations started not to appear in the downloaded version.

To Reproduce
Merging a big ontology file into an existing one in a project in WebProtege V5.0 may create the bug. We tried in multiple projects and we could not reproduce it every time.

Expected behavior
We expect only a single download file that is associated to our Ontology in Development. Plus, we expect all our changes in Editing Mode to be reflected to the download file consistently.

Desktop (please complete the following information):

• OS: Linux/Windows
• Browser: Chrome
• Version 5.0