Not to mention that, since it is all just a bunch of stories anyway, those stories aren't going anywhere. As long as you can still watch the episodes and movies and read the old books, nothing's been "erased."
I see this argument made a lot, like when DC wiped out their continuity from the last few decades. But some of the value in stories like Star Trek comes from the knowledge that the characters continue on after the show/movie ends.
Watch the final scene of the TNG finale. Now imagine that right after the episode ended, the entire universe blinked out of existence. Doesn't that take away from the warm fuzzy feeling you get? The feeling that this family is going to continue on, possibly being closer than they were before because of Picard's experiences -- that's gone. Sure, there's plenty of other stuff to enjoy, but one major element is gone.
That's why people care whether stories "count" or "still exist." It's not because they worry their DVDs or comics might disappear. It's because part of what the value from those stories may be gone.