It would make sense to me that re-embarking would also carry over the seeds that have been unlocked for farmers. You’ve got recipe unlocks and, as you play, you can unlock other seeds from traders. I highly doubt that the farmer wouldn’t want to bring all his seed options with him to a new place. No one likes the same food over and over.
Also, because it can be a PITA just to unlock them to begin with, it’s a minor accomplishment in the game when you finally get that ONE kind of seed you need. If you fought and struggled to get something, you’re not going to leave it behind when it’s time to move on.