In The Flash season 2 finale we saw Barry travel back at time to save his mother from Eobard. This means the writers just followed the Flashpoint storyline where Barry travels back in time to save his mother and succeeds but gets a Post-Apocalyptic Present in return. He loses his powers, most of the Justice League Member do not get their powers or they died and Aquaman and Wonder Woman starts World War 3. After getting his speed back he travels back in time again and changes everything. Everything comes back to normal yet a bit changed.
Maybe a same thing will happen with The Flash. Maybe after re-changing the timeline Flash may get a new suit, new base, new ally but I still love Caitlin and Cisco, Harrison Wells (Real one, not face taken by Eobard or Earth-2 counterpart) return, Cisco's full power, Wally's Super Speed, Henry Allen remains alive etc etc. You know what I'm saying.
Rip Hunter's Team are bunches of idiots. Instead of letting Snart sacrifice himself, they could have sent Firestorm to absorb the Blast Radius. If Firestorm could absorb Entire Blast Radius of Nuclear Bomb, then he can absorb enough to become more pwerfull. Or they could have just put something heavy to put the Fail-Safe switch inside or use a Duct-Tape. I mean did they had to kill Snart.