For quite a while I have been using GoodSync (made by the fine folks at RoboForm) to sync my RoboForm files between my USB flash drive and my primary desktop PC at home. I would then manually copy files between my flash and my home laptop. Tired of that, and understanding that I could easily make a mistake, I decided to look for a free sync tool that functioned like GoodSync but wasn't as pricey.
I found SyncBack (http://www.2brightsparks.com/). It works basically the same, allowing one to exempt files and folders that one doesn't wish to sync; in my case, I exclude *.rfo files (which means any files that end in .rfo), due to them being RoboForm license files that must stay on the PC to which they belong. To ensure SyncBack's file exclusion filter actually works, I first copied both folders -- one from the flash and the other from my PC -- to two temporary folders, then synced them up. Sure enough, the *.rfo files did not move...did not over-write each other in the other folders, and all was well. I then repointed SyncBack, to the real folders, synched them, and I was happy.
Give it a shot if you need to sync files between two folders. It works great between a local PC and a network folder too.