Hello Robert Pell,
Please try to delete the VM instance manually using below Azure CLI command and let us know if it fails/throws any error:
First get the Instance ID of the VM which you want to delete using below command:
az vmss list-instances --resource-group <your-resource-group> --name <your-vmss-name> --out table
then try to delete the VM with the instance ID using below command:
az vmss delete-instances --resource-group <your-resource-group> --name <your-vmss-name> --instance-ids <instance-id>
Alternatively, you could use Powershell command too:
Remove-AzVmss -ResourceGroupName "Group002" -VMScaleSetName "VMScaleSet002" -InstanceId "<instance-id>"
or if you are just looking to reduce the VM instance count from the VMSS, you could try scale-in operation on the VMSS.
Sample Azure CLI command:
az vmss scale --resource-group <your-resource-group> --name <your-vmss-name> --new-capacity <desired-instance-count>
Let me know if it helps to delete the VM instance!!