After restarting the VM with ArcGIS Enterprise 10.9.1, access the ArcGIS Admin Directory and then:
Go to services > Hosted and find the Scene service that is not working.
Stop the service.
Start the service.
After restarting the VM with ArcGIS Enterprise 10.9.1, wait 15 minutes and restart the ArcGIS Server Windows process. This fixes all the scene layer services.
Publish a new scene layer package file (.slpk) as explained in the Workflow in Steps to reproduce.