For instance, I like the bleakness of Alien 3 opening with Newt and Hicks both dead. That doesn't spoil my enjoyment of Aliens, which ends on a triumphant note. These are different stories, and they can be treated on completely different planes. If you want, you can imagine the movies as representing alternate branching universes, where one branch led to Newt and Hicks dying in hibernation, and in some other branch that's too uninteresting to be put to film, they live happily ever after.
I also liked Blade Runner 2049, but I don't need to retroactively reevaluate the original Blade Runner in light of any of the questions that are settled in the sequel. In Ridley Scott's original film, Deckard's humanity is still open to question, regardless of what's presented in Villeneuve's version.
Of course when the sequel is complete trash, it's easy to ignore entirely. Terminator 3 being the obvious example.