I found something by reading the source code to wyUpdate on google code
This works from a batch file:wyUpdate.exe /server="file://%~dp0\wyserver.wys"
You have to copy the .wys file and the .wyu files into the same place.
All together in the same folder:1) this batch file with that one line in it2) the wyserver.wys file3) the .wyu file4) the application to update (the .exe of your app)5) wyUpdate.exe6) client.wyc