I don't think anything has yet been changed which has any real significance, with the exception of Sylar's reversion to evil.
Future Sylar was a good guy and had a son, probably with Elle. If there has been a change in the timeline, that's the one that has significance. Future "Good" Sylar destroys Costa Verde and that leads to "full weaponization" of the formula. That event would appear to no longer be in the cards.
So whatever lead to that odd flip-flop and fip-flop back of Sylar's "alignment" is probably the only real event that has significance. It might be that the scene in the car rental shop with Elle which seemed so utterly random at the time was the product of time-line interference. Not sure, obviously.
If that event was the thing which tipped the balance in favour of Syler "becoming evil", then the resulting death of Arthur Petrelli last night through Sylar might also be key.
We know from how this Chapter began that Future Peter had a scar - and that Future Peter had regained his powers.
So we know that the events of last night, and in particular, the fact that Peter had lost his powers, and that he received a scar was always "supposed" to happen. (Athough, I seem to remember the scar being on the other side of his face.. I may be wrong about that.)
We also know from the fact that Future Peter had his powers that he gets them back at some point. Hence, we know the Catalyst worked and that next episode or a few after the next one, Peter will take the perfected formula and be restored.
What we don't know is how everything goes off the rails. I think that the choice which Peter faces is the one that the Chapter began with. Averting the future was never about stopping Arthur Petrelli... It just looked that way. It was, in fact, always about stopping
Nathan Petrelli.
Nathan will have to back down and stop the spread of the formula - or someone - probably Peter - will have to kill him... for the third time.