Ok, so I thought of this storyline and thought I’d share this with you guys, it’s not completely flashpoint but keeps lots of elements.
So, Barry wakes up and notices everything is different, the big changes, him and Iris barely know each other, Henry Allen is in prison for attempted murder on Nora (form the night Barry came back), Barry is still working CSI with Joe, forming a further bond, but Francine never left, and Wally is The Flash (in the kid flash suit). Barry figures out who the flash is easily and goes to star labs to figure things out. Cisco, Caitlin, Ronny and Wells (Not killed by Eobard) all act normally, Cisco has his powers but is still in early stages of learning them, Caitlin and Ronny form Firestorm, and Wells is in a wheelchair from the car crash that killed Tess Morgan, for real. They all know of Barry but he didn’t know about Wally’s identity, he tries to tell them about the old timeline and they all brush it off except Cisco and wells.
Over the next few weeks (time skip) Barry proves that he knows Speed extremely well and how to use it, he tells the team of his tales but they all think it’s bull, and wouldn’t be able to prove it otherwise. But Barry hears stories over time about the Aggressive ‘Arrow’ and his vengeful methods, so Barry goes there to investigate thinks he’ll meet Oliver. There he meets the arrow, Malcolm Merlyn (since John Barrowmen is a series regular, I think this is the most likely to happen). After Barry is able to prove enough things to Malcolm he agrees to help him and they make way to star labs.
Albeit angry at Barry for bringing Malcolm, they begin to theorize how they can make communication with the other Cisco, because the timeline that Barry left is still there, but without their Flash, and this Barry is living in another timeline, so both timelines are going parallel. This Cisco is able to glimpse into the other timeline, but not able to see everything. And this leads into the original timeline, where Cisco, Caitlin, E-2 wells and Jesse (now with her speedster powers) are all figuring out where Barry went, Cisco is able to know he’s in a different timeline/Earth, but unknown where. Until he is able to see what nobody else can, another Cisco looking in though a hole, but the breach closes before he can question it. This rupture in the timeline leads to the black flash (from the set photos) coming after Barry. This scene essentully happens (https://www.youtube.com/watch?v=OJ1lqBzw7c4), and Barry gets his powers back, making the black flash even angrier. Wally has to deal with the black Flash and the Cisco's figures out a way to talk to each other. They figure out that if enough kinetic energy is built up in one place at a singular time on 2 worlds, the Cisco’s could open a breach between the worlds. Since Barry and Jesse both got their speeds back, they decide to do it, but the black flash comes along and adds in his kinetic force, which allows Barry to go back home, and the black flash into a different timeline.
I know this destroys how flashpoint can Change the timeline, just an idea I came up with and thought it was an intrusting take.