Ok so i have a theory on all this.
The night barry's mom was murdered, there was up to 4 barry's there
1. Kid Barry
2. Barry from Season 1 Final
3. Barry from Season 2 Final
4. Future Barry
Well all know why barry was there the first 3 times but the mystery still remains on the fourth time but i have a theory.
After the season 2 final barry returns to the future and finds himself somehow powerless and in an alternate timeline (Flashpoint Paradox) after regaining his speed he finds eobard thawne after his apparent death in the season 1 final who explains the theory of the time boom and that is how eobard is alive, after all the events of the flashpoint paradox, barry time travels back to the night his mom now didnt die and he restores the timeline. After this, the timeline goes back to normal and barry warns team flash that thawne is still alive and he will be season 3's big bad.
The reason i think this is because in the season 1 final, #4 future barry puts out his hand to barry and shakes his head for barry to not save his mom and i think that it is because that is the barry that has just prevented the flashpoint universe frome ever existing.
This theme could last for a couple of episodes because of the crossovers and this cant effect the other shows.
Now another theory is that by saving his mom, barry has just created earth 2 and then cisco could open a breach for him to return.