An interesting question KingDaniel. I agree that Michael Dorn's movie is probably a long-shot, but if it does happen and is thus declared canon, I'd like to think that all of the current storylines would be wrapped up and then a new separate era with the new status quo would begin.
Failing that, you could have some huge galaxy-wide crisis which results in the giant reset button being hit. This will likely be the preferred route, go out with a bang, not a whimper.
I'd like to think that Dorn, aware that he was making a small scale, possibly short lived project would set it in a small part of the Trek universe so as not to contradict other stuff. Yeah, like that would happen...
If there's not much conflict with the novels, a clever novel retcon or two may solve the problems.
If Dorn's project stamped all over novel continuity a big (and hopefully elegant) retcon to cleverly reset the continuity would be my choice rather than going off in its own direction, which probably wouldn't be allowed anyway.
I'd ask Christopher to take it on, but don't know if he would be interested...