Within the Application Manager console it is not possible to remove an endpoint from within Endpoint Analysis if the Application Usage scan is enabled. This is by design and the recommendation would be to stop the scan prior to deleting the machine. It is worth noting that the endpoint must be turned on in order to stop the usage scan as otherwise you will see the following error message:
To resolve this issue, the endpoint should be turned on and the RPC (Remote Procedure Call) service should be running.
If the endpoint no longer exists, please review the following article: