Eobard Thawne's sudden appearance surprises me a lot, he dies, and then again reappears. But what's the specific explanation of him showing up during the Crisis on Earth X crossover? I remember him indirectly referring, being the Reverse Flash of Earth 1 during the crossover, but what the heck is he doing on Earth X? And why's Tom Cavanagh playing Matt Letscher's role?
It's because the events in Flashpoint
An alternate timeline, coined Flashpoint by Eobard Thawne, was created by Barry Allen when he traveled back in time and saved his mother from the Reverse-Flash. The timeline was reset when the Reverse-Flash ran back in time and killed Nora Allen again, restoring everything pretty much to how it was before, albeit with some minor differences. However, after Barry Allen used a superseding form of speedster time travel to live in this timeline's version of 2016 for three months, he found the world much different to the timeline that existed before, with Cisco Ramon becoming the genius industrialist instead of Harrison Wells and Tess Morgan, Wally West becoming The Flash instead of Barry, and The Rival becoming a new menace of Central City
The Flashpoint timeline can still be accessed by those with dimensional awareness even though this timeline was reset by Eobard. This was shown when Cisco vibed into Flashpoint to determine Clive Yorkin's next victim. The victim was thought to resemble a cop in Flashpoint.
Changes between the Pre-Flashpoint and Post-Flashpoint timelines
- Joe West and Iris West became estranged for a time due to the revelation of her mother being alive.
- Dante Ramon died in a car accident caused by a drunk driver. (This may have happened during those three months regardless of Barry's time traveling.)
- Caitlin Snow developed meta-human powers exactly like those of her Earth Two counterpart, however this resulted in her developing a cold personality as well. (This may have happened during those three months regardless of Barry's time traveling: it's possible that Caitlin had gotten powers from the Particle Accelerator explosion in the pre-Flashpoint timeline too and they simply hadn't developed yet.)
- S.T.A.R. Labs now has a speed lab where speedsters can train.
- The members of Team Flash now have "panic buttons" installed on their phones.
- John Diggle doesn't have a daughter anymore, but a son instead. In addition to the gender difference, Diggle's child was also born a month later in the new timeline.
- Julian Albert started working at the CCPD as a CSI in late 2015. He also inadvertently released Savitar several years prior, and unknowingly became Alchemy as a result.
- The future has changed, one specific change being Iris getting killed by Savitar in the future before the year 2024, with the future newspaper article instead being written by Julie Greer.
- Ralph Dibny, who previously was one of the fourteen people who lost their lives in the particle accelerator explosion, is now alive.
Additionally, the following events occur as a direct result of Flashpoint:
- Alchemy is able to restore the superhuman abilities of seven meta-humans who only had powers in the Flashpoint timeline: The Rival, Magenta, Shade, Clive Yorkin, Wally West, and two other unidentified people.
- The Dominators launch an invasion of Earth, as they are alerted to Barry's time traveling and seek to prevent Earth's meta-humans from doing further damage to the universe.
- The time remnant of Eobard Thawne (with memories of his 'future' as Harrison Wells) escapes to the present. He finds himself pursued by the Speed Force's ultimate enforcer, forcing him to stay for temporary amounts of time whenever he time travels. He attempts to further alter the timeline to change his fate, eventually leading to the creation of the Legion of Doom.
And of course, since things've changed, Thawne may not be dead as we thought he was. He is very much alive and seeking for revenge from barry
Major spoilers for everyone, dear people. This will decently explain the whole mess on the Flash-LoT.
Flashpoint Eobard becomes Wellsobard (without flawed Speed Force connection); when Eddie kills himself Eobard avoids erasure and goes in the Speed Force. He goes to 2000 and brings Barry back to 2016. Then Eobard goes to LoT; he is sent in the Speed Force by Black Flash. He escapes when Barry escapes from the Speed Force and appears on the Earth X crossover.