You can download Creative Media Source off the Creative support website if she lost the install CD. (if this is in fact the problem)
Apart form that, I'm pretty sure Media Monkey syncs with the Creative line up. I know it does with Apple's offerings as well as my iRiver (as if I needed software to sync with my iRiver), so I see no reason as to why it wouldn't with her Zen Micro.
Just out of curiosity, MaloS, I don't doubt your scenario's validity in the slightest, but why would you ever remove the battery while it's on and running? Did you do this by accident or something? The Micro's battery is lodged pretty well in there if my memory serves me right. I mean, it's been probably over a year since I've owned one, but I thought the battery was a rather non-issue for me.