http://yabb.jriver.com/interact/index.php?topic=51734.0Does 2-way rating sync.
For flacs you'll need to set up handheld folder in MC that points to the itunes library folder.
This way there are mp3's for itunes to use.
Then you'll need to create a field iTunesFileKey in MC with a calculated value similar to this:
Replace([Filename (path)],\\NAS\Volume_1\mp3\,E:\Users\zxsix\Music\iTunes\iTunes Music\)Replace([Filename (name)],flac,mp3)
This maps the mp3 in itunes with the matching flac file in MC.
In the options of the sync utility, you need to check the box for alternate file key.