Ahhahahaha. I have a similar story to that, but I eventually realized what happened.

I forget which command it was exactly, but I rsync'd or something to get a new code directory, and with the backup options in use the directory I was in got renamed.

But I still had command prompts open in that directory. And all of the files were there. So I didn't realize that one directory was not equal to the others even though it had the same name (it was a subdirectory) and appeared to have the same files.