Hello
Perform a synchronizable P2V and instruct Converter to stop the Notes service(s). It will do so right before the sync. If you can allow - schedule the sync in off hours. Users can use the source machine during the conversion.
You can also schedule the synchronization as non final, test the VM, then do a final sync. The service will be stopped only before the final sync.
And of course - do not decomission the source machine until you have verified everything is OK with the new VM.
HTH,
Plamen