@psycho_soldier: Not the Thomas of that Earth certainly, no. He must be dead, or Bruce wouldn't have been Bats at all. I believe, though as mentioned by someone else, Taylor could be changing the plans, that it was implied that this is in fact the Thomas Wayne from the Flashpoint timeline, notice the similar costume motif and behavior. That's somewhat backed up by his reaction to someone mentioning Bruce.
The question then becomes how he survived the merging of all the splintered timelines and made it to Earth 2. But hey, Superman is an insane god of destruction right now when he was allegedly dead on Earth 2, so Bats is hardly the only big question mark right now.
Another issue is that this Batman is apparantly Super human. He stopped punch from Red Tornado and took a bullet to the head. I don't remeber the cowl being strong enough to tank bullets from a few feet away. I don't see how this is flashpoint Thomas or the one we know at least.