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If you are running both instances on the same server using a different port offset you will need to make sure the service knows that. For instance, if your applications has a port offset of 100, include the flag /controller localhost:10090 when installing the service (the default port is 9990). Otherwise it may connect to the wrong service and shut it down instead.
Thanks for the advice! i retried and point to the correct controller localhost and am able to shutdown the wildfly server correctly now Thank you!