Well, DCAU resource put it this way "The Flash was still puzzled why he still retained memories from the Flashpoint era. As he mused it was a temporal after-effect, Batman interjected and remarked it was a gift." Since Batman and Flash have different suits and Batman is voiced by Kevin Conroy, it would seem to imply that either Flash returned to the OG timeline seen in the beginning of that film or he's in a third timeline we haven't seen since this scene. When he enters the speedforce at the end, it's possible he goes to the New 52 timeline and all of his memory's wear off since he mentioned it was "temporal". Just a theory. Either way, it's difficult to figure out exactly. Head-canon may have to be the best way.