I had learned that bay always changes when followed by pronouns in the following way: ban mwen, ba ou, ba li, ban nou, ba yo. But sometimes in Istwa Jezi pou timoun they use "bay" like this: "Abraram te konn bay Bondye kado. Li te konn bay li bèt." The first bay makes sense to me because it's followed by the name Bondye. But I would think the second “bay” should be just “ba” because it's followed by “li”. Is there a reason that it doesn't change to ba here? Or can you substitute bay for ba anytime?

If I was writing this paragraph I would have used “ba” in the second sentence because that’s what it should be.  You may have found a typo there.

Haitian Creole ↔ English Reference, Look up Haitian Creole and English Words