I think that's probably their intent.
From a chronological standpoint - the current timeline had to exist for them because, if Eddie kills himself to prevent Eobard from ever existing - then Eobard couldn't kill Barry's mom, Barry wouldn't be the flash (at least at that time, theoretically), and Eddie wouldn't be in the position to kill himself to keep Eobard from existing, so in the redux universe, Eddie would still exist, not kill himself, and the cycle would repeat.
Therefore, if you want to believe in the multiple universe theory, at the point Eddie kills himself, a universe is created where Eobard never exists and the prior events all occurred AND another universe is created where Eobard never goes back to kill Barry's mother.
The universe they stay in is likely an abnormal universe or fractured or something as Barry cannot exist in his current form without Eobard still coming into existence to become his enemy and one day go bcak and try to kill his mother.
It could very well be that a number of new universes were created to balance out all the potentialities of the situation and the singularity we saw causing damage was the universe at large doing just that.
