This Novell article:

http://www.novell.com/coolsolutions/appnote/14729.html

Seems to discuss how to install and use a minimal package that installs the cygwin rsync utility. The UNC path is effectively a local drive, and a cygwin utility should work directly with it without you needing to map it to a drive letter (although you could do that in a Perl/Batch script anyway). Since you only want local syncing there's no need to run the rsync daemon, just use it as a commandline tool.

Syncing file structures efficiently can be a tricky problem, so rsync will save you a lot of work. A big benefit of using rsync in this case (rather than replacing the files every night) is that you will be making many less write cycles to the memory stick, so it will last a lot longer.