There's an incredibly useful-looking script on here
http://fedoraproject.org/wiki/LiveOS_image
that merges a LiveOS snapshot overlay into a new root filesystem, and replaces it on the USB stick, so that you get all your overlay space back. I've been looking for such a script for a while.
Is it included in livecd-tools? Or any other Fedora package? (I'm reluctant to run the script on the web page, because I'm not sure how well tested it is.)
The script appears to claim that it can cope with being run from the USB stick itself, while it's booted up, which sounds too good to be true (or, at least, too good to be safe).
James