The players I've always had never really cared about a character mysteriously popping in and out of existence, just the occasional joke of "Hey, where'd that guy with the shiny purple gloves go this time?" Of course, the players I run with tend to be goofy types, so most of them didn't feel a huge need to have everything make total sense in-game.
Realistically, you'll rarely (if ever) be able to seamlessly fit a player's attendance record into the game world--someone has to leave due to their master's commands halfway down a dungeon and comes back (one missed session later) after the group's done three fights and solved the deadly puzzle trap, which may have only taken an hour or two in-game. "Yep turns out he just wanted me to put this scrying mark on a tree outside. And no, it couldn't have waited three hours for us to finish what we were doing." However, if your group really gets into that kind of immersion, it can become a practice in creativity--explaining why and where they're gone while leaving it open how long they could be absent.
Edit: the bigger issue as a GM is making sure you can balance encounters on the fly depending on whether your extra character is there or not. You don't want to make it so everything's a breeze because she's there or extra difficult because she's not. Of course, with it just being one player it shouldn't be that drastic, but an extra minion or two you can add in would probably help balance it.