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Sometimes when I open gamemakerstudio 2, some files are duplicated in the asset section, sometimes they get mixed up in the other file, it's very annoying, and when I click on it and delete it, they both get deleted.
Try exporting the project and importing into an empty project. Always make backups too.
If it persists, I think it's best to try submitting a bug report, because I've never seen this happen before.
Kind of funny, as Duplicating entire folders+content is one of the workflow feature I so wish GMS had!
Definitely not normal, I'd try clearing cache, restarting machine, and if all else fails, reinstall GMS.