Well, sadly, no. But with what's revealed you can easily get out of it that if Gene had been doing his job properly, that wouldn't have happened as Sam should have gone back at the end of series one when his issues were resolved and not all that time later. But at least Gene didn't remember his job, so it's kind of excusable, and it's implied that from now on, thanks to Alex, he will remember his job and be a better cop heaven ferryman. Yeah, so poor Sam got a bit screwed.

And the Annie closure was that it was mentioned by Keats that she was missing in that universe and nobody could find her, which means she entered the pub-that-is-heaven with Sam.