In an earlier story draft I had Renet and Big Lita more explicitly die, they were eaten by Armaggon, but during the writing process we decided to change their fates to being more ambiguous. In my mind they're both gone, but maybe another writer will have it so they escaped at the last minute through a portal or something like that, so you never know! Even if they did get eaten, maybe their molecules could reconstitute somehow. ;)
For Little Lita, I actually drew her as a turtle in that final scene initially, the original art has her as a mutant, the implication being that when Donatello destroyed Future Bob's QNA-absorption device, the QNA went back into the universe where it belonged, but eventually I decided no, it shouldn't be that easy. Lita should bear the scars of what happened and the QNA that encodes her mutation should remain inside Future Bob so he'll always remember. However, we've already seen Big Lita as a mutant arrive from a point in time after she's been de-mutated, and in keeping with the causality loop stuff in my final arc that must mean that somewhere along the line during the 20+ intervening years, she's re-mutated. Maybe we'll see that story someday.