If there are no files in the pin folder then that means you went too far during the switch device wizard. Follow the instructions very closely. If you cancel out or continue on, the files will be removed from the folder. After it reads the 3rd party apps, do NOTHING. Just go find the folder and copy it to another location. THEN go back and cancel the switch device wizard.
This procedure was not meant for doing this but is a workaround way to backup all 3rd party apps at once. Good luck.