Seeing as what DCTV has announced in terms of their shows next season, there are a few small clues to what might happen. This whole Flashpoint timeline would be assumed to affect shows across the CW, but as someone said, they can easily have a self contained arc with Ollie's dad, etc.
But then that becomes an issue when the time comes for the annual Flash/Arrow crossover. Granted if Arrow continues on its on time, and Flash is Flashpoint, there's no way the two will crossover. But then it was announced earlier this month that there will be a super-crossover of Flash, Arrow, LOT, and Supergirl. That might actually be the (multi-part?) episode that Flashpoint gets resolved.
Keep in mind, Flashpoint, if it's anything like the comics, would bring back RF as the villain AGAIN. And this time it will probably be full Eobard Thawne, not Harrison/Thawne. I'm not sure of the idea of another speedster being the big bad, let alone a repeat big bad, is a good one. And chances are I doubt CW would spend the budget to recreate another show (Arrow) from the ground up to match the Flash's consequences. Although this does give writers and producers a golden opportunity to retcon the entire CW and get rid of things fans don't like (Laurel's death, Olicity, etc.) and bring back things they did like (Laurel alive being the one true BC) as well as merge Supergirl into CW-verse. And characters in LOT can be unaffected, since they're pretty much independent from the timestream at this point, unless the writers choose to (bring Snart back). Will the CW have the balls to do it? Only time will tell.
