The only “project backup” is the one I listed above. To my knowledge there’s no other options or function built in RapidWeaver that would do what you said happened.
I personally never use the backup option, as I have a complete backup strategy of everything on my computers including offsite storage. But I have run tests on the built in backup and it appears to work fine for those that choose to use it. Turning it on and off seems to work as well.
Just like the rest of RapidWeaver’s publishing function it doesn’t delete anything on the server(a good thing) including the backup and associated directory. So if you’ve turned it off and you wish to delete the backup you have to do that manually with a ftp client or your hosting file manager.
If what you deleted wasn’t within that unusually named directory It didn’t come from RapidWeaver bult-in backup. Since you didn’t say what the file name was or where on the server it was found, it’s difficult to say where it may have come from.
Does it reappear on the server each time you publish?