Leave them all in. Remasters are for restoring a work to as close as possible to the way it was meant to look when it was released, and nothing more. You wouldn’t look at a painting by da Vinci or Vermeer and say “Hey the perspective is off there,” or “That kind of bird doesn’t belong in that time and place,” and then “fix” the painting in the process of restoring it.
The creator(s) made a series of decisions during the original process of creation. Maybe some of them were mistakes, but they were their mistakes to make, and not anyone else’s to try and second guess after the fact. Once you start down that path, there’s nothing preventing George Lucas style special edition madness.