It's never actually stated in canon that she left the ship any more than it's stated that Chekov transferred to security during the 5-year mission - that's an assumption based on his role in TMP. Janice is seen as a CPO assigned to engineering (transporters) in TMP, so a similar assumption can be made that she simply moved departments and treat her as a PO under Scotty's (or Lt Kyle's) command.
In fact, we never see any other yeomen billed as Captain Kirk's personal yeoman rather than the occasional generic yeomen in the later episodes so it's entirely possible that Janice was still on board, just not involved in any of the stories.
Still, a return to the Enterprise following additional training like Ro Laren could be a plot device, and a useful way to establish some skills for the character that give her something more to contribute to the story than making the coffee. Mind you, don't underestimate the importance of preventing the Captain from getting cranky due to caffeine withdrawl!
NB: Her non-canon reason for leaving the ship from the novel the Captain's Daughter (and mentioned again in Ex Machina) was that she was pregnant but her daughter later died from an illness (aged 2 I think)... that's something I've decided to touch on when I do part 2 of my Youtube comic but the timeline also fits in year 5 if you decide to use that! She seems to tell everybody that Annie's father died, although she is vague on the details so there is some speculation on who the father could have been...