As mentioned in https://jira.magnolia-cms.com/browse/MAGNOLIA-9175, I'm opening a support ticket here because the issue is still persisting for us.

Steps to reproduce

1. Module Folder Structure:
   Module-Name/src/main/resources
     /Module-Name: contains templates, dialog configs etc
     /Module-Name-Theme: contains JS/CSS/Fonts etc.
2. Navigate to Resource Files App

Expected results

1. Filter by "css" or "js" and be able to patch any files

Actual results

1. Filter by "css" or "js" and see that the JS/CSS files from the theme are no longer listed here

Workaround

1. Navigate to JCR App
2. Select Resources workspace
3. Add root node of type mgnl:folder with same name as Module Theme Folder (module-name-theme)
4. Navigate to Resource Files App
5. See that the folder containing the theme files (css, js, fonts etc.) is now visible in the Folder Tree
6. Filtering by "CSS" or "JS" now lists these files again and I am able to patch them.

Development notes

The last working version for us was 6.2.26. Upgrading to 6.2.40 from 6.2.38 does not fix the issue.