As I posted in another Flash thread:
Because Eobard killed her in the past, that event will be unchanged because Barry didn't stop it.
Eddie killed himself, so I assume all the Thawnes of the future have been wiped from existence. By all time travel movie logic lol, only an event in the past can affect the future.
He was marooned in the year 2000, making it plausible for his (Thawne's) actions to still have effect. As his ancestor was killed in the present day, only the future is altered - if any of that makes sense.
There are multiple timelines at play in the show.
1) The season 1 timeline (Nora Allen's death to present day)
2) The future (where Thawne/Reverse Flash exists and Red-Suit & White Logo Flash exists)
3) The alternate future (Where Barry saved his Mom).
4) The future without the Thawne bloodline (after Eddie's death)
You might think how I know there's an alternate future where Barry saved his Mom. Well, if you think about it, why did Future Flash signal to Barry to NOT save his Mom? Why else would he do it? Obviously when he saved her, he disrupted the timeline and events played out differently. So in a way, they've acknowledged "The Flashpoint Paradox" without going in to great detail.
There could also be a way for Thawne/RF to be resurrected in the show. Say in future seasons there is an event that they can't deal with and they need the help of Dr.Wells/Thawne. The night he killed Nora Allen is still in continuity, since he was stuck in the past. As the finale said, he had 1 minute & 52 seconds before the wormhole closed. It closed, trapping RF in that timeline. So that event will most definitely always be in play. What's to stop The Flash from returning to that night or pre-Eddie death timeline and taking Wells/RF with him?
That's my suggestion for bringing back Tom Cavanagh anyway LOL!