We can then simply imagine that they found a way to do it off-screen.
Problem solved.
A lot of the stuff were not mentioned on-screen to begin with that were done in the novels (not canon, I know - but still).
Perhaps, but ignoring the issue because it's inconvinient it's poor writing doesn't matter if it's in a book/film or TV episode. It's almost like a Deus ex machina.
It's not my fault as a viewer if they call attention to something and later ignore it, I can rightly call them on their sloppy writting. As I indicated the issue is more them ignoring the issue rather than issue itself, and addressing these issues could easily have been done via a log entry. Doesn't really impact the casual viewer but acknowledges to the segment of the audiance which pays attention to these things (and SF fans are known for paying attention to details) that we know we said this but we are changing the playing field (for lack of a better term).
Of course by the time VOY aired, internet usage was becomming far more common so the ability to perhaps get away with these things was narrowing. As newsgroups etc.. allowed people to discuss the episode perhaps far more than they could previously.
Blame the writers for the inconsistencies.
They were the ones dumbing down SF's technological capabilities as time went on.
I was just mentioning what seemed more than possible for the Voyager crew to have done off-screen (think self-sufficiency - literally every SF ship in the 24th century with transporters could do it even with low energy reserves) to explain the inconsistencies the writers introduced.
Granted, doing the 'dirty work' for the writers doesn't seem like it should be done, but people try to explain things away in a logical manner that does fit in-universe and possibly has more credibility.
To further this analogy... the Bussard Collectors were originally intended to be used as collecting stellar matter and use it for energy generation.
As such, the purpose of using Deuterium as 'fuel' seems to fall apart (as I have to ask, what purpose is there to having to use 'fuel' when SF ships and equipment mainly need potent energy source to run them)?
The main source of power on board is the Warp core which needs anti-matter (secondary power sources apparently include fusion reactors - as well as impulse reactors, though these might have been mentioned as being a part of the impulse engines).
It was mentioned on-screen in the early seasons that Voyager's core can function for 3 years before having to be refilled... and evidently, they managed to solve this issue long before it became an issue (either via omicron particles, or they managed to synthesize it themselves in uninhabited star systems, or they traded for it).