When you have stopped you sap instance you may well need to restart the sapstartsrv services.
You can do this by sending a nice kill to the pid if you like, but sap do provide the syntax to do it with stopsap.
just issue the command
This will restart the startup agent for all the instances.
Please not that this will stop the instances that are owned by these services, you will need downtime to restart sapstartsrv!