User blog comment:Thegamingknight4272/Flashpoint Question/@comment-6015011-20160805150557/@comment-3423279-20160806001504

Eobard didn't change the timeline all that much really, he just moved events up.

Barry on the other hand has entirely changed Earth 1 with his time travel.

It might be that the amount of changes one causes between timelines results in memories either staying the same or gradually changing.