Yeah, the TNG Dominion War books are hard to reconcile with Ro's later appearances because one or two scenes. They don't outright contradict each other, but it's certainly odd to reconcile twice and be cool with the first time and be pissy the second time. (Though you could say, Picard was mad Ro didn't come back to SF, etc., etc.) I'm unsure of the comics, as not too many tackle the TNG movie era. And I don't recall specifics, I have to read through them again.
The TNG Dominion War books do also have other little hiccups. They heavily imply Taurik is dead, but he's hale and hearty in the A Time To... books. Geordi has a visor in the story for some odd reason, too.