To stop him they need to stop him from existing in the first place.

Now that we know how Savitar was created there is the issue of how to beat him because no matter what Flash does Savitar will already remember it from experience as it’s part of a closed loop which will end with Iris dying and Flash going into depression and stopping him only after creating him. But there is one way to stop it which will probably get Flash killed or banished into the Speed Force but there is nothing he won't do to save Iris so I can easily see him going through with it. He needs to go back to the night Nora died and change the timeline again by stopping his own younger self from ever interfering in the first place and restoring the Pre-Flashpoint timeline.

Julian Albert

Julian's very presence is proof that Savitar didn't exist before, as he would have been around during season 2 if he did.

There are several indications that there was no Savitar in the Pre-Flashpoint timeline. For one Savitar himself basically confirmed it as he was created to stop Savitar only to become Savitar. Second Julian Albert wasn’t around during the Pre-Flashpoint timeline at least not in Central City but in the Post-Flashpoint timeline, he’d been working for the C.C.P.D. sometime near the beginning of season 2. We now know this is because Savitar possessed Julian and moved to Central City because he remembers the encounters with Savitar from his own past, and was just playing out the script so he could become Savitar. Also Iris' death is also further proof because Savitar exists as a result of Barry's own broken nature because Savitar ruined his life but he couldn't have existed if Iris never died.

Barry's future suit

I still think Barry is going to become the future Barry inside the house, and I say make it this season.

During Flashpoint Eobard Thawne convinced Barry to allow him to change things back and while Eobard is a lunatic we know he values self-preservation so we knew he was telling the truth. That said his very intervention changed things yet again and led to the Post-Flashpoint timeline and I think Eobard did this on purpose. I don’t think he anticipated the creation of Savitar but I think he knew Barry’s life would be different and we know Eobard will take any chance to ruin Barry’s life. I think Barry is going to have to go back and stop his Season 2 finale self from entering the house and I think that this will be when Barry becomes the older Barry who fights Eobard inside the house, discourages his season 1 finale self from interfering, saves his 11 year old self and vanishes. I think then after doing all this Barry is going to go back to the house and intercept his season 2 finale self before he can stop Thawne, speed him away and Eobard will continue as planned without knowing of Barry’s previous intervention. That way his timeline is restored to its Pre-Flashpoint state.

Killer Frost (Caitlin Snow)

Come on, tragic as it is, this was going to happen with or without Flashpoint.

This may sound like it will make the entire season a bit redundant if they just change everything again, though to be honest this season has been a bit of a letdown anyway, but there are still several things that I think will remain regardless. I still think Caitlin and Wally will be Killer Frost and Kid Flash because Caitlin was affected by Eobard’s accelerator and I’m like 95% sure that was going to happen anyway. Wally was given his speed by Savitar but he was also affected by Harry reactivating the accelerator and I think that his current Speed Force connection is actually a combination of that and the Philosophiser’s stone, so while he wouldn’t be as fast as he is now he wouldn’t be powerless. I also think Dante’s death will remain because his death occurred several months after season 2 ended and Flashpoint altered the circumstances of Zoom’s defeat so that it occurred several months after it actually did, so all that stuff with Cisco and Dante being attacked by Earth-2 Dante would have still happened. 

Hunter Zolomon and the Flash in the Speed Force

Still think this is how the season is ending. It would also be kinda ironic as Hunter's actions led to Barry creating Flashpoint.

However, and I’ve been saying this for months, despite Barry restoring history he will have broken his promise to the Speed Force yet again and I think it will dispatch the Black Flash after him and it will either kill him or imprison him in the Speed Force as punishment for his actions. I don’t think Barry will stay gone but I think the team should have a few episodes where Barry is gone and they have to protect Central City without him. I think this could also be a good time to adapt the “The Return of Barry Allen” storyline, but I won’t spoil it for those who haven’t read it which I recommend. This is just how I think the season will end because Savitar seems to be impossible to defeat and quite frankly I don't want the season to end in another round of Barry gets faster to beat the villain, so at least this would be more creative.