The Legends are the ones responsible for bringing Thawne back to lifeThawne himself claims he came back because "time travel is confusing"; and we know that Legends breaking time resulted in countless anachronisms, so why shouldn't Thawne existing when he shouldn't be one of them?
Eobard Thawne is the one who helped the Nazis win WWII on Earth-XThe reason the Nazis won the war on Earth-X is because they developed the atomic bomb first. We know that Thawne tried to get the Nazis to the same in the Season 2 premiere of "Legends" so what's to say he didn't do the same when he got on Earth-X.
- Or on the flipside, Earth-X's history is what inspired him to try the same during "Legends".
The Time Masters are responsible for the Nazis winning
- The reason the Time Masters helped Vandal Savage on Earth-1 was they needed a strong and united Earth to fight off a future Thanagarian invasion. To their minds, it might make sense that a world under Nazi rule has a better chance of fighting those aliens and thus justifies letting humanity live under this rule.
Next Year's Crossover Will Merge Earths 1 and 38
- Thawne fights Superman in the future. While he could just travel to Earth 38, why would he when Barry doesn't exist there? It would be more likely that the Earths end up merged into a single one. This works on multiple levels: it would streamline future crossovers; it would allow Thawne a chance to exist without time-travel shenanigans (Eddie could still be alive on Earth 38); and it would return the CW multiverse to a proper 52 Earths, including the newly introduced Earth X.
- Alternatively, he was just lying to intimidate Kara. Or he discovers that there is a Barry Allen on Earth-38, and goes there to kill him just cause it would upset the heroes. Or both.
Whether Or Not The Above Guess Happens, What Will The Next Crossover Be About?
- Crisis on Infinite Earths