The teams excluded (or left behind) from the Super 6 would remain the Division 1 schools from the NCAA. The WAC, the Mountain West, the Sun Belt, Conference USA, and the MAC would consist of approximately 48 schools for football.
For basketball, I’m not going to list all of the remaining conferences, but suffice it to say, that the NCAA basketball league would still be plenty strong (particularly the new conference of Big East outcasts or the conference that absorbs some of them). It could initially still rival the Super 6 for quite some time. The remaining 271 Division 1 schools would still create compelling basketball nationwide, even if the 74 Super 6 schools would garner the largest audiences. Eventually though, the financial advantages of the Super 6 would relegate the NCAA schools to a sub-class of hoops.
From here on out, when I refer to the NCAA, I’m really talking about these remaining Division 1 schools.
Goodbye NCAA 
The NCAA could not really survive without the top teams. They’d become the NAIA part 2.
They’d still have their Division 2/3 schools. Too many schools overall to completely go belly up. They’d need to restructure their finances, for sure. But they’d still have enough members and income to survive in some form.