WebStorm repeatedly marks all files as "not listed"

My project conatins several branches, which I keep swapping between.

Once in a while, about once daily, swapping to a branch (not any particular one, happens randomly) would mark all project files yellow. The Project Tree would then only show files directly in the root, and none of the subdirectories:
Though it still sees them in the directory:

 

Looking through some posts and online, I cannot find a solution that solves this issue. I tried "Invalidating Caches" but that just didn't do anything, restarting also doesn't help.

The only thing that solves this issue when it happens is deleting the .idea directory, then restarting WebStorm, which recreates the directory and apparently re-lists all the files again.

I'd love to resolve this permenantly, if anyone has any idea why this keeps happening.

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Hi there,

If you share .idea subfolder via VCS then try removing and excluding it there.

Looks like one of the config files gets somehow "corrupted" and the IDE now treats all files as "outside of the project" (the typical yellowish background on files in the Project View panel (it will be light yellow if using Light theme)). Deleting the .idea subfolder while IDE is closed (and then re-creating the project from existing files) is one of the ways you can use resolve it once this happens (especially if you do not have a backup/previous working version of it).

I suggest you make a backup copy of .idea before deleting it and then compare it to the working version. In particular: compare .idea/modules.xml file content -- the paths that are used there (they can be different due to VCS actions, especially if this project actively used by other WebStorm/other IDEA IDEs users working on this project).

Do the above the next time this will happen and share your findings here.

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