The Big 12 is at worst the 3rd best football league and ranks as the #1 basketball conference.
There is no process to take away their autonomy designation. It's foolishness to think they'll lose status with those metrics.
As for the NBE, that option could have been initiated at any time. That league was never saying no to bringing in UConn, considering that all of their members are so much weaker than UConn. They don't get much money and UConn helps them more than the NBE helps UConn.
UConn could've easily waited to see what the AAC looks like coming out of realignment, to THEN decide if it was time to give up on P5 status, aka autonomy.