You might be right about some shifting around. I don't have a great handle on where all of the possible future DII schools are and the conference affiliation possibilities.
The one underlying thing that is likely to drive this is money (surprise?). We see the issue in D-1 conferences that are spread out all across the map. Those schools tend to have significantly more resources at their disposal. I just don't see it working for DII and NAIA conferences. They just don't have the resources. I could see some schools just dumping the whole athletic department.