I know that in the final season Mork and Mindy went back to prehistoric times. Now my question is did they ever come back to modern times?
We don't know but it's implied they would...
The cliffhanger ending to Season 4 was intended to kick off a change in direction for the show in Season 5
“We even tried to get a fifth season. So here was the scenario: [Kalnik], another alien, became Mork’s buddy, and then [Mork] finds out he’s there to kill Mork for some reason. And so, to fend off this threat, they revealed themselves to the public [as an alien and his wife], and ultimately they had to run away through time to hide from [Kalnik]. It was going to be a semi-educational show, where Mork and Mindy traveling through time would meet with historical figures. We actually did a photo shoot for that, of [Mork and Mindy] standing with Abe Lincoln and Benjamin Franklin.”
Unfortunately, the show was cancelled and the "final" episode "The Mork Report" which had actually been filmed before the 3-part finale was shown out of order to give the show a more appropriate closure feel.