I don't think it would be that hard for Comcast to get those rights though. And it won't take six flags a lot to retheme what they have except for maybe their new joker dark rides.
You underestimate DC"s presence in six flags parks. Here in Texas they are opening an entirely new Gotham area this summer. A Catwoman's Whip ride, a Harley Quinn spinner, and a Riddler's Revenge coaster. This fits in with the already installed Batmans and Freeze coasters. The same goes for every other 6 Flags park, the DC/Looney Tunes licenses are the last ones they have after giving up all the rest around 2010.
Is retheming possible? Sure, but at what cost? 6Flags over Texas alone would have the retheme nearly a third of the park, most of it being brand new. The cost of retheming every single on of their parks, along with the lost revenus of having these attractions closed in the process and the lost value of having licenseless rides, and the lost sales of DC merch are all big pills to swallow.
So sure, it's possible, but why would Six Flags want that to happen?
Now, if Warner Bros absolutely wanted to pull the license from Six Flags, they actually can. They have escape clauses in their contract, and the only reason Six Flags HAS these licenses to begin with was because they used to be ownded by Time Warner.
Either way though, you have to assume Universal would actually want to
A: Give up rights to the, undeniably, bigger brand
B: Take 1/5 of IOA down for a complete refurb/retheme for a good portion of a year or more
C: Want to tackle something like this when they have major construction plotted out to 2020 currently
D: End up giving Disney something back they can then roundly use to attack the exact same demographic that Universal has leads in - teenage boys and young men.
Consider these notions as well:
*Hulk will have just reopened when these negotiations start
*Spider-Man can't simply be "rethemed". A whole new movie, ride motion, sets, queueu, etc have to be built in
*Universal turns over a ton of merch currently. They'd have to walk away from all that
*There have been strong rumors that they are actually going in the opposite direction and *adding* rides to the area.
*The value of something like the DC license is heavily hinged on the performance of Batman vs Superman and Suicide Squad. If they don't do well (as in amazing), you can kiss any chance of DC getting out of Six Flags goodbye.
*Even if Disney got Marvel, the best anyone can hope for over the next 4-5 years is some rethemes, parades, and M&Gs. Their construction schedule is pretty full right now. And there won't be a 5th gate just for Marvel, which means you get to have it shoehorned into an existing park. Considering MK is at near capacity, DHS and AK are getting huge upgrades currently, that means Future World is where it would most likely get dropped. Proceed to riot.