Or maybe they justs fudged it because they figured the average fan wasn't keeping score. Ever noticed how the hero in most action flicks would need about five lives to survive the movie? Same thing here. If everything on Voyager actually happened, they would have needed about a dozen ships to survive the series.
That's pretty much how I interpret it. I like the concept of Voyager and I like the stories. I don't like how the writers seem to be less invested in it than the fans and the actors.
They could have talked about consequences or about permanent changes to the ship, it wouldn't have been that hard. I think that was one of the reasons BSG was so appealing. What's odd to me is that there is a good deal of continuity in the series so far. I don't like that they save it for Deus Ex Machina situations while kind of taking for granted the technology. It's one of the things I'd like them to change in future shows: stop making some technology more primitive (scanners, engines, weapons) while using replicators and stuff to wave away all of the stuff that is actually pretty necessary and usually thoroughly explained in any sci fi.