Hey Jonathan,
You would need to add debugging and/or logging to your Windows service, because that's where the problem is, so long as you're doing these 3 steps:
- Adding the service file(s) to wyBuild so that they will be patched & updated correctly.
- Stopping the service before the update.
- Starting the service after the update
Also, if you get any errors from wyUpdate please tell me the full error. (Copy & paste).