One big question is if the unification preempts all Time Traveler's Immunity somehow. It's a completely speculative question relying on our own understanding of internal logic, and the attempt to cover it in Chrono Cross Resolutions can easily go over one's head...it was tough to write.
But I guess what happens with TTI is, Masa, Mune, and Doreen all come back in with...well, nevermind. I was going to say that the trip to 1015 A.D. to save Kid would give them TTI and qualify them as coming back, but Serge would arrive at that point to. He'd be Time Bastarded mercilessly, but even this is taking it too far.
Without TTI, the short answer is that Chrono Cross's ending is a giant void.
So, essentially, like with everything else after Chrono Cross, we have no bloody idea and all of our theories and speculations are all for naught. Damn it but we need a new Chrono game! So many questions left unanswered...so many theories created for this and that...
Still, I would have to say that the reunification does not rewrite Time Traveler's Immunity but it all depends on whether the DBT was aligned with any specific point in time or not. If it would be aligned with anything, it would be either 12,000 B.C.--the moment of Schala's entry--or 1999 A.D.--the moment of Lavos' entry. If it is the former then any case of Time Traveler's Immunity after 12,000 B.C. is ignored because the entire timeline is completely rewritten. If, however, it was 1999 A.D., then all Time Traveler's Immunity cases for our heroes apply.
Of course, it could also be aligned with 1010 A.D., the time of the Dimensional Split, in which case once again, Time Traveler's Immunity cases are rewritten, and all events proceed from that date.
But what is far more likely is that it is not aligned with any particular date or time along the timeline, and as such the entire timeline is rewritten in some fashion, with all Time Traveler's Immunity cases ignored yet again.
...as I said, this is all speculation with no real basis in anything but our own theories which in and of themselves are occasionally shaky, though at least unlike theories I've seen for other games they are quite sound on the whole.