I have a folder where I direct my backups. It is set in Options. After importing a compile setting, the next backups made will the saved to the CompileSettings folder, unless manually changed back to the preferred path, even though, in Options, the correct path is still indicated.
I would report this as bug. But it really just seems to be the way Scrivener works, when it comes to the file system and pathing, and the (often very unfriendly) dialog boxes we get for interacting with the system (interactions that, in this case, were made necessary because of the way Scrivener’s pathing settings work.)