The fix for made in the commit
here causes all existing raster uploads to be deleted when the scheduled importer cleaner task is run in the JobQueue class because existing upload directories do not contain the .locked file thats used for checking.
This commit might also cause issues for cases where you're using the importers import from directory feature since you might upload to that folder from an external app and not have a .locked file created there (though you could just create a .locked file from your app).
A clean way to fix this might be to have a separate ".clean-me" file created for all new uploads and the cleaner task ignores any upload folders without it. This would avoid any messiness with a migration script for existing installs and solves the second minor issue with uploads from external services neatly.
(We actually have our own upload cleaner script we wrote separate from geoserver to solve this and upload files separately and use import from directory in the importer rest call. Just removing this new code from a forked geosever repo fixes it for us completely so I'm not going to fix this myself and don't need it fixed for us I just felt you guys might want to know about a potential user data deleting issue)
I see. Your suggestion makes sense. I'll take a look at this as soon as possible.