Why are Dabura and Babidi alive in the future?
The future timeline already diverged from the main timeline when Trunks saved Goku. Think multiverse theory. Nothing that happens in the past has affected the future. That's the reason Cell existed in the future, even though he was killed in the past. It's also why all the characters remained dead, even though they were alive in the main timeline.

That considered, the future timeline had its own unique past, where Babidi and Dabura weren't killed until they encountered Trunks.