I remember playing through Oblivion again and you all can remember that particular quest involving the elder scroll to turn back time and rewrite history right? Well.. I always hear about how the Dwemer are gone.. kaput.. dead (aside the one that was not on mundus when it occurred). With that said though.. Couldn't the elder scrolls bring them back and rewrite history?

Highly doubtful. The Dwemer aren't so much dead but rather part of the Numidium, which at this point really isn't all that affected by timey-wimey shenanigans, it pretty much does its own timey-wimey shenanigans. I doubt Akatosh has enough of a hold on it that you even could undo it, the Dwemer basically severed themselves from the Mundus in a lot of ways when they popped into Numidium. The Jills would probably kick your ass themselves if you even tried to bring back the Dwemer, because they've had their hands full whenever the Numidium's been a thing, having to constantly somehow fix the timeline or at least come to some compromises just so the timeline's somewhat workable when the Dragon Breaks end.

I'd also shy away from interpreting the Thieves Guild quest as directly using the Elder Scrolls to re-write time. It was something of a complicated interaction of the Grey Cowl, Nocturnal (who, being a Daedra, is outside the normal flow of time anyway) and the information on the Scroll. It created a very isolated break which did nothing more than change a single event.