Since I wrote this, the events of “Convergence” — yet another mega-event — took place to correct this. Not by making it clear Barry didn’t destroy all those universes — he totally did — but by having Brainiac save little fragments of them so they could rebuild in a way that let them say “never mind!” Thanks in large part to the Post-Crisis/Pre-New 52 Superman, because that’s what Superman does.
At no point does this absolve Barry, mind. It just serves to extend an olive branch from DC to the rather large number of people who stopped reading their comic books. Which doesn’t seem to have worked, which is unfortunate.