That opens up its own fork in the road concerning whether or not Flashpoint affected Earth-3, and whether or not Jay even knows who Barry is.
The Flash’s dense story structure allows for several different scenarios that would allow Barry and Jay Garrick to team up during Flashpoint.
(And that starts up talks about whether Harry and Jesse would remember their Earth-1 adventures, and so on.)
One way could have Barry facing a huge problem that could only be helped out by another speedster – a third one, I guess, considering Kid Flash is also around – and the Scarlet Speedster has to zip over to Earth-3 to talk Jay into assisting.