Great question. That exact thing happened in the Conan (1982) Blu-ray.
There is an early scene that was shot during the middle of the day where Conan is being chased by a pack of wolves. In post-production they darkened it so it would seem to be just before dawn and imply he was being chased all night.
When they restored the elements they didn't know or realize this and transferred it as a day shot. So now he be being chased at high noon by the dogs and the original intent was lost.
I don't get how mistakes like this happen. You'd think a requirement for remastering/transferring a film would be watching the original.
Look at some of the behind the scene from TNG-HD, you almost always see an editor with both the newly scanned film and the original tapes for comparison.