To answer your questions: Yes.
Voyager had really bad continuity in many, many aspects of the show. I mean "Fury" literally changed the first three seasons of the whole damned show. The writers were only interested in telling a fun and interesting new sci-fi story each week which they mostly succeeded in, but that's really where their ambition ended which was a pity.
RE: Lindsay Ballard, no they weren't in a relationship but her existence as Harry's close friend on Voyager makes absolutely ZERO sense and that detracted from an episode which has one of the best concepts of any Trek show ever.