Maybe they forgot their history. And then Lily regained those memories/history and understood that the 19 kingdom alliance and imu are the evil, and once again allied with soyboy.
Like, there must have been a reason for Lily to turn traitor against the 19 kingdoms and fuck them in the ass by spreading the poneglyphs. So that's probably it.
Also, the "fake" alabasta history that robin read off the poneglyph to deceive crocodile might actually have been the real history of Alabasta. It was said to be from 3000 years ago or something.
So Lily read those and figured it all out.