HOLY TIME MASTERS BATMAN! there is so much being teased in this issue. first, this is taking place in what is not the alternate timeline of Flashpoint…no this is likely taking place in a flashpoint Universe-S (stabilized). Darkseid’s omega beams did not kill Thomas Wayne, they Sent Thomas back threw time to his own universe which would have been created when the 52 returned to being an infinite number of worlds when the hands restored the multiverse after Death Metal. the original FLashpoint-universe was not its own universe but an alternate timeline however The convergence event made it its own universe, however, Thomas Wayne became a living paradox like Thawne after Thawne pulled him from the original alternate timeline Dr. Manhatten was maintaining.
As Thomas is a ‘living paradox’ like Thawne was he does not realizes he was sent to what was now his home universe in the multiverse. meaning it was Flashpoint-universe S’s Barry Allen and not New Earth Barry Allen who was killed.
however… it also revealed the time masters are going to interfere in Batman’s past…my hopeful theory is the TM’s changed Bruce’s past so BATMAN GOT MARRIED TO CATWOMAN! as this event was actually altered due to Thomas’s presence in the universe.
there is a lot going on behind the scenes that is only now coming to light, as Thomas says people were coming after him when he arrived on President Superman’ Earth…that could have been the Amazons and Antlantians or someone raiding Arkham.