Hey there @Manostion! Welcome to the community. This is a bit of a weird one! I’ve seen some project files be disassociated before, usually because some of the metadata files got left out of source control, but since it doesn’t seem like you’re using that we’ll try some things.
Try backing up your project by making a pure copy, then delete these folders in it and relaunch:
these will be regenerated (but also hold your cached data which is why we backed them up).
If that doesn’t work, launch the duplicate project, remove everything from the content folder, let it register it all as missing, then close, replace everything in the content folder and relaunch. This sounds a bit odd but it’s worked before for file re-association.
If that fails we might have to try some other things, hopefully avoiding having to drill down into manual content replacement, but that’s the literal worst case scenario.