Correct - the idea was to use zotero as an simple way to carry the references on a flash drive, and be able to run it on any _PC_ that you may use (desktop/laptop). It doesn't exactly "solve" the sync issue, unless you just want to backup the flash drive every few days. If there could be an efficient parser to process the directories, you may be able to generate a "file listing" that was easy to navigate from within Zotero.
To address the sync issue:
What about using rsync under cygwin? I personally haven't tried it, but here is a link:
http://www.gaztronics.net/rsync.php
and more info:
http://www.itefix.no/cwrsync/
Windows used to have some sync tools - how about SyncToy:
http://www.microsoft.com/windowsxp/u...o/synctoy.mspx