First, I can't buy into the notion that Harry was an ensign for the rest of his career. It's a great cruel joke, but it's not realistic. We've seen him promoted in multiple alternate realities, after all.
Upon Voyager's return, its crew evaluations were transmitted to Starfleet, and promotions were handed out wholesale. Naomi got to stand on a box and pin senior lieutenant pips to her mom's collar. Harry got a second gold pip as well, and Tom took him to the real Sandrine's, where they had a promotion party and both got super drunk. B'Elanna had to retrieve them from the local drunk tank, and gave Tom an earful for it.
The Maquis crew were pardoned by Starfleet, but they were cautious about assignments. B'Elanna became a Federation liaison to Quo'nos. Tom was assigned to the shuttle design division. He had a very spotty record, but his sheer brilliance and family connections allowed him a moderately successful career, after which he became a holonovelist. Chakotay taught anthropology at Starfleet Academy. His relationship with Seven went nowhere, but since they were no longer in the same line of command, he and Janeway kept in touch and soon began seeing each other.
Harry rose through the ranks steadily but not spectacularly. As a LCDR, he served on the Enterprise as Captain Worf's operations officer, and was later upped to first officer. Inspired by his commander, he began wearing his own hair long (because I like Garrett Wang's new look).
I'll have to think about the other characters...
