I have similar files with just numbers in the folders that I synchronize. I've been using SyncToy for quite a while now to synchronise folders on my laptop with 'mirrors' on a remote server, using a VPN connection. I haven't tried via a pen drive.
My strategy is to always have the latest version of folders locally and simply to back them up to the server. If the laptop fails, I could get them back, one way or another.
However, a while back somebody (sorry, can't remember who) posted that they seemed to have lost stuff whilst using SyncToy to transfer things backwards and forwards - i.e. using it in both directions. I haven't tried that but take care if you do!