Since Flashpoint occurred, I've always wondered about this question. Since Barry basically created the Flashpoint universe and then reset everything by stopping himself at the end of the event. Does he retain all of his memories of his life in the prime universe? Moreover, since one of the very first things he did was visit Bruce, does Batman acknowledge that Barry is basically from an entirely different universe?
Yes, Barry has the unique distinction of having been at the center of the Flashpoint paradox. He may be the only person to remember first-hand what happened there. Will the memories be retained (or will he even want to remember) has yet to be determined.
Wikipedia confirms this in its Flashpoint entry:
Traveling back in time, Barry merges with his earlier self during the attempt to stop Thawne. While traveling through time, Barry realizes he can see three different timelines — DC (New Earth), Vertigo (Earth-13), and WildStorm (Earth-50).
A mysterious hooded figure (later reveals to be a cursed immortal Pandora) tells him that the world was split into three to weaken them for an impending threat, and must now be reunited to combat it. The DC, Vertigo, and Wildstorm universes are then merged, creating a brand new DC Universe.
Barry then wakes up in a similar manner to the beginning of Flashpoint, also retaining all his memories from the alternate timeline.
Believing that everything is over, Barry remembers Thomas' letter and gives it to Bruce, who is still the Batman in this timeline. Bruce, deeply touched by his father's sacrifice to ensure his son's life, tears up after reading the letter and expresses gratitude to Barry for informing him of the events that transpired before the timeline was reset. (REF: Johns, Geoff (w). Flashpoint 5 (August 2011), DC Comics)
Yes, this means Batman knows there was a continuity other than this one. He has proof of the other continuity in the form of the letter from Thomas Wayne. Could the memories be recovered by magic, telepathy or super-science? We simply don't know. It is likely Batman is considering that right now...