To reset syncing between Yojimbo and Simplenote, do the following:
Quit the SNYS application if it is active, as well as any other application which syncs with either Yojimbo or Simplenote.
Make sure you have a set of notes in either Yojimbo or Simplenote which you want to keep, and that the other is empty.
To overwrite Yojimbo from Simplenote: just clear the “Simplenote” folder in Yojimbo, either by deleting the notes entirely (probably best) or moving them out of that folder.
To overwrite Simplenote from Yojimbo: leave Yojimbo as it is, and delete everything in Simplenote. If you have a lot of notes this can be annoying to do manually – I have written a “Delete all Simplenotes” script which can make this easier.
Launch SNYS again. It will clear out all of the previous sync pairing information automatically, and re-sync your notes. This may take a while initially if you have a lot of them.