By its nature The Flashpoint would have changed nearly everything. I imagine if The Reverse-Flash never killed Barry's Mother and spent the subsequent years in a cell then the Singularity that drew Zoom's attention to Earth-1 never occurs and Zoom's rampage on Earth-2 continues uninterrupted. I don't think it was ever clarified if he had access to other earth's but he did know of their existence, so perhaps his madness on Earth-2 carries on until he finally burns out... of course poor Jay Garrick will either be killed by the despairing Zoom or dies of starvation in the glass cage. Though on the other hand maybe Harrison Wells(2) is galvanised to develop the strategy that finally ends Zoom?
Zoom would have been left to conquring all of the worlds in Multiverse, until he got to Kara one, and Supes and her would have kicked his butt!