I don't think there ever were any problems, Andre just didn't wanna rap no more. He was on Andre's solos and even did production so he was always around even after the last album. Now they can't do anything together unless it's an Outkast album for contract reasons.
The only public issue was Big was upset they missed out on STUPID amounts of money from not touring during the Speakerboxx/Love Below era. Thats the only time Big has ever publicly complained about Andre’s behavior. Andre even addressed it on Sorry the T.I. Song.
Members of the dungeon family also said that the two were dissing each other on Mighty O but thats never been confirmed.
And Andre can work with Big Boi and be featured on tracks with him if he wants to, Big Boi has publicly said all that red tape has been cleared up.
Andre just don’t want to rap unless he’s super inspired. And apparently he’s only super inspired once or twice every few years. And there’s nothing wrong with that, it is what it is.