Nothing says it has to be acrimonious.

One extremely feasible reason is that he was too busy. He's been very hands on working with Rapsody. He was making/coordinating one last album with MURS. He's probably working on lots of other stuff right now. Given the seemingly aggressive timeline to get this done and out, he might not have been available.

Another reason could be Phonte and Pooh wanted to go in a different direction. They could have been feeling the beat that Khyrsis played or made for them and decided that was the type of sound that they wanted.

Or it could just be that Phonte & Pooh and 9th decided that they were in different places artistically at the time they were recording this. Think De La Soul and Prince Paul: Paul became less and less involved with the group as time went on (especially around "Buhloone") because the Three Plugs became more comfortable moving the group in their own direction. There was never any "beef" or hard feelings, but just the sense that they wanted to move on.

Or it could be as simple as 9th didn't feel like he wanted to get reinvolved with a group at this particular moment. Even these days, making a commitment to being a member of a group is a big deal. Maybe he didn't think he could do the press for it, tour, etc.

So, basically, we don't know the reasons, so we shouldn't assume that there's any bad blood here.