User blog comment:Bo-Katan/Thawne and Time Remnants/@comment-27673963-20171209080014

This is how I see it.

Wells/Thawne is erased in Season 1 but to stop paradox's they continues Thawnes existence but everything from his birth up until he first time travels is in a timeline that no longer exists, so he is erased because he can no longer be born but his younger self exists to stop paradox's from destroying the world. After Flashpoint, Thawne creates a time remenant and then leaves to Legends Season 2. When Black Flash catches him in the Finale, he isn't erased he is taken to the speed force and is barred from going to Earth 1 so he goes to Earth-X and the Earth-X villains create their own way of travelling through the multiverse so that is how Thawne returns.