I know it sounds like a dumb question, but did you try rebooting the PC?
I was getting a different error after I uploaded my 3DN files to google drive and tried to re-open them again. It would say that there was a sharing violation on the file. Shutting down 3DNes and exiting Google Drive didn't work. The only way I was able to get it to work again was to reboot my laptop.
I would really have a hard time believing that you wasted hours of work as long as your backup 3DN remains unchanged. If rebooting doesn't work, I would uninstall and re-install the emulator and see if that worked.