No, the comics gave Kirk temporary command of the Excelsior after TSFS, because Paramount asked DC not to do anything that might conflict with plans for the next movie. So DC set up a placeholder status quo where Kirk was temporarily given the Excelsior and the revived Spock was given command of a different ship so that he wouldn't interact much with the rest of the cast. When the time came to lead into The Voyage Home, they did a storyline that undid those changes and reset the status quo. Nothing was "rendered invalid"; it was all done in coordination with Paramount and designed to dovetail with the movies.
Although it didn't quite work, as it turned out, because the storyline leading into TVH, by Len Wein and Gray Morrow, erroneously assumed the Klingon Bird-of-Prey was small enough to have been carried in the Excelsior's shuttlebay the whole time, even though earlier issues by Mike Barr, Tom Sutton, and Ricardo Villagran had correctly shown the BoP as large enough that it had to be tractored behind the Excelsior, tucked into its aft undercut.
That's the exact same situation. Nothing "happened" to them, because the writers and editors of those comics coordinated with Lucasfilm and made sure not to cover any story areas that might conflict with the moviemakers' plans. That's why the comics rarely had any confrontations between the main cast and Darth Vader, and why their storylines focused mainly on original situations, species, and guest characters rather than things that might be covered in the movies or that Lucasfilm specifically asked them to avoid.
Yes, Naraht appeared in a couple of issues that Duane herself wrote for the comic, as did other of her novel characters like Harb Tanzer and Lia Burke.
"Where No One Has Gone Before" was written by Duane and Michael Reaves. I believe it started with Reaves coming up with an idea that he realized was similar to The Wounded Sky, so he asked Duane to collaborate with him. But the TNG writing staff rewrote the script so heavily that hardly any of Duane's or Reaves's work remained.