My iPods recommend building Banshee 0.9.11.1, which has three major fixes, two of which are iPod fixes that make syncing work without crashing (huh, what a concept). Also some minor UI tweaks to make things look pretty slick.
So just for kicks, I ripped a purchased CD, MusicBrainz fetched the info and Banshee fetched the album cover, then I synced the ripped tracks to an iPod, then I burned those tracks from the iPod back to CD, then I imported the CD again... no loss of metadata. I'm sure the quality dropped a little, as the flac->mp3 conversion does nasty things, but you can bring that up with Apple.