Today I had some problems and had to go to a zipped up backup file.
My intention was to exit Scrivener, rename the current folder to CurrentFolder.old, then unzip the backup. However, even after exiting S and all other apps, I couldn’t rename the folder, being told that some app was using it. I had to reboot.
Scrivener releases the project as soon as it’s closed; you shouldn’t even need to restart Scrivener to trash or rename the project’s folder. It sounds like something else on your machine had this locked, or you experienced some other temporary glitch. If it happens again, you could check to see which processes are locking the file and try to trace it that way.