Because they're different productions, they have different writers' rooms. I know people like the idea of a connected universe, but they're really only connected for crossovers and small cameos. Flashpoint rebooted the entire DC universe. They're not going to invalidate years of storytelling on every DC show on the network for a season finale stinger. Not everybody watches every show.
The other shows would have to do storylines for however long this thing with Barry lasts, and then it will all be undone. Making those stories pointless. No character growth, no meaning to revelations, etc. You can do it contained on Flash because (ideally) Barry should grow and learn from his experience. It will test him. But the other shows having different versions of their characters for an event they can't resolve would be bad tv storytelling. It works in comics for big events, but these shows don't crossover like comics.
Also, the reasoning behind everything changing in Flashpoint has always been iffy in my opinion. I like the storyline, but that one changing effecting past events that occurred before Nora's death...eh. Little too Time Wimey for me.