First of all, sorry for my English... And, if you haven't seen both "Out of Time" and "Rogue Time" episodes of The Flash, please stop unless you don't care about spoilers
Have you thought why Barry sees himself at the moment he travels in time at the end of "Out of Time" and at the beginning of the same episode? You could say "of course, he is seeing his "future" and "past" self in each moment respectively. Well, yes, but, why there aren't two "Flashes" in "the past" after Barry travels? Here's where my theory comes around.
We've seen Barry only sees himself at the moment he travels or "is travelling", but then, in both moments, his other self disappears, it can be because at that moment he's "breaking" or "dividing" the space-time; at the moment he travels he creates an inconsistency on the space-time, so, like Wells (Eobard) says, the time tries to fix itself, it implies there can't be two "Flashes" around there, so, an alternative timeline is created at the moment Barry travels, the moment when this timeline is being created is the same moment when Barry sees himself. After that, the "Out of Time" beginning Barry continues in his timeline and the events we saw in the whole episode occurs, and the Barry who have traveled continues in the new timeline and the events we saw in "Rogue Time" occurs. So, what happens in the "Out of Time" timeline after Barry travels and creates the "Rogue Time" timeline?, we could say Barry disappears from that timeline but the time there is still running, and the Harrison Wells (Eobard Thawne), Caitlin, Iris, Joe and basically everyone from that timeline continue with their lives, wondering where is Barry.
All of this implies we have now at least two different universes or timelines on the DC TV Universe, turning it into a multiverse, and those two different timelines applies for both "Arrow" and "The Flash" shows, so in the future we could have an encounter between both universes; in one of them Cisco is dead, Iris knows Barry's secret and Caitlin knows that Harrison Wells is not just a scientist, and most important, there's no Flash; and in the other universe Captain Cold knows Barry's secret and he have new weapons. I don't know how it can affect the "Arrow" plot, but it would be interesting to see a multiverse encounter, maybe between those two universes or maybe between more after the "Flashpoint" events which seems to be coming to "The Flash".