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We recommend using the pisrvstop.bat before shutting down/restarting the OS. A lot of times end users will just restart the OS and things end up fine on the system, but using the script is another level of safety for us in making sure everything gets shutdown in the correct order. As for starting the PI Server. The services are by default set to automatic startup and already have their dependencies in place, which means that you won't shouldn't need to run the pisrvstart.bat script on a start of the OS.