To be fair, they didn't explicitly say "we're recreating the old universes instead of restoring them". That's too much existential angst for DBS. But it's the Star Trek teleporter issue - the universes did not exist at all, no afterlife, complete oblivion, for a brief period. Then the super dragon brought them back. But is there any continuity between the original and restored universes? Did Zeno just fake their destruction because he was running a secret test of character and knew the winner would wish them back?

The existential angst is explicit in Trunks' scenario, because he knows his universe ceased to exist and the time clone is a clone. But Trunks always suffers. It's part of being Trunks.