Board Thread:The Flash discussions/@comment-13895380-20170103171048/@comment-24152851-20170103223353

It's how Jay Garrick explained. When you break time and try to fix it, you can't restore it to exactly how it was. It's like fixing a broken mug, there will always be a crack remaining.

It's likely that since Eobard was aware of Flashpoint and had to go back and change the past, he knew about his fate at the end of season 1 and had it play out differently. I think the LoT Eobard didn't bother with the Harrison Wells stuff and went straight to teaming up with Darhk.