I would consider using a version control like git. If your network is slow it may take a while the first time, then subsequent updates should be fast as only the changes will be transferred.
You could also just setup a GIT repo on your thumb drive and update to/from that repo on your work and home computers so as not have to copy all of the files every time. It doesn't have to go over the network, though you will likely have a much greater degree of integrity with regards to the actual version control using a network solution.