My F150 needed a reprogram after a new battery was installed. But with a dual battery setup, the truck never loses power, so that step can be skipped. As far as going from FLA to AGM type, it shouldn’t make any difference in the system. If you went to lithium there might be an issue, but AGM is fine.
Both of my stock FLA batteries show signs of leakage, and I was thinking of going with AGM as well since they are sealed.