Something similar happened to me once. I still don't know what exactly happened, but in Dropbox some files were deleted, I still had my local copy, but then Dropbox synced the file deletions and I didn't notice. Only when it was too late did I notice that files were gone and their support was unable to help. I think I managed to recover some files with one of the NTFS "undelete" tools, but that was probably the day I started to treat "the cloud" differently. Nowadays I don't even know what's still in my Dropbox ...
I was clearing out Dropbox when I moved away from it, and it _wouldn't_ let me delete my copy of `tex.web`, because it thought it was some sort of special dropbox file. (It was the source to TeX.)
It's been a few years, but I think I managed to delete it in the web UI. (This was on macos, and they had a kernel extension keeping an eye on things by that point.)
