I agree, and outside of "Jetrel", how much of any of this was really dealt with?
It's not like I expect multiple episodes with him in physical therapy or anything, I'm just saying that the loss of the lung did not affect the character in any way from that point forward. If someone skipped "Phage", would they even notice, other than for Janeway's two-second reference and Neelix's correction of her that someone mentioned earlier.
In some ways, this is just the flaw with episodic storytelling. Voyager was basically an anthology series with the exception that the main characters were the same every episode, but almost nothing mattered episode-to-episode.
Its just a freaking lung, what did you expect them to do exactly? Write episodes about how Neelix is out of breath? The lung that is left adjusts and becomes stronger, Neelix would hardly be at any disadvantage in his daily routine.