I always patch manually like this:
- Update the master server
- copy the contents of master Windchill/codebase/CCSTools/update/ to remote file server Windchill/codebase/CCSTools/update/
- restart Windchill on the remote file server
- Occasionally Windchill will need to be re-restarted because it has an error in extracting and applying the updates.
If you have test servers setup, to test the patching on before hand, can copy the "precopied" contents from "test remote file server" Windchill/codebase/CCSTools/completedUpdate/ to "production remote file server" Windchill/codebase/CCSTools/update/ for step 2 above. If you have a slow WAN connection this can save you time.