User blog comment:ReverseZoom101/Plotholes that I noticed in season 3 of the Flash./@comment-24152851-20170903105615

1. The Flash's logic is that a character who gets erased from existence will still exist, up until the point where we see him get erased. Nate explained that on Legends. Savitar was needed to reach that point in the timeline, so some form of him would have been preserved by the Speed Force.

2. I think they just did it once with the explanation "we see HR, everyone else sees Randolf" and decided it's done and just keep using Tom Cavanaugh and pretend it never happened.

3. Probably some other Particle Accelerator explosion. The original Harrison Wells caused it in the first timeline, but Eobard made it happen earlier so it's likely someone did in Flashpoint too.

4. Either the trees were moving at super speed thanks to Savitar or Wally wasn't moving at top speed at that point.

5. Same reason as my first answer. Savitar's gone, but his presence is still felt. He was still there in Season 3 even if he's gone afterwards.