Azure Managed Run Command stuck in Deleting with 409 conflict

This can require backend cleanup if the Managed Run Command control-plane operation is stuck. The documented self-service actions supported by the context are:

1. Check whether a Run Command is still reported as active.
   • PowerShell:

          Get-AzVMRunCommand -ResourceGroupName "AXIOMQUANT-RG" -VMName "AxiomQuant-Build"
          Get-AzVMRunCommand -ResourceGroupName "AXIOMQUANT-RG" -VMName "AxiomQuant-Build" -RunCommandName "AxiomQuantRepoLocal" -Expand InstanceView
     

   • This returns the deployed Run Command resources and, with -Expand InstanceView, the latest execution state, output, exit code, and terminal state.
2. Attempt deletion of the stuck Managed Run Command resource.
   • PowerShell:

          Remove-AzVMRunCommand -ResourceGroupName "AXIOMQUANT-RG" -VMName "AxiomQuant-Build" -RunCommandName "AxiomQuantRepoLocal"
     

   • Azure CLI:

          az vm run-command delete --resource-group AXIOMQUANT-RG --vm-name AxiomQuant-Build --name AxiomQuantRepoLocal --yes
     

   • REST:

          DELETE /subscriptions/<subscriptionId>/resourceGroups/AXIOMQUANT-RG/providers/Microsoft.Compute/virtualMachines/AxiomQuant-Build/runcommands/AxiomQuantRepoLocal?api-version=2023-03-01
     

3. If the resource remains stuck in Deleting and new requests continue to fail with 409 Conflict, treat it as a stale operation that is not clearing through normal delete.
   • The context includes a case where a stuck Run Command operation in Cancelling was resolved only after backend removal of the stuck operation.
   • That matches the described condition: control-plane state remains blocked even though Guest Agent health is normal and no active execution is visible.
4. For Windows Run Command troubleshooting, review the extension log on the VM for evidence of an actually running or failed handler operation:

      C:\WindowsAzure\Logs\Plugins\Microsoft.CPlat.Core.RunCommandWindows\<version>\RunCommandExtension.log
   

   Also check for these known blockers:
   • reserved characters such as & in parameters that are not escaped
   • paths containing \n
   • custom HKLM\SOFTWARE\Microsoft\Command Processor\AutoRun settings
5. If the log does not show an active execution and the delete operation does not clear the resource, the supported next step is Microsoft-side intervention to remove the stale Run Command operation.
   • The context shows that stuck Run Command operations can require backend removal.
   • In that state, further self-service retries are unlikely to succeed while the platform still reports run command extension execution is in progress.
6. Avoid extension removal unless specifically using it as a troubleshooting step.
   • If needed, the action Run Command Windows extension can be removed and will reinstall automatically on the next Run Command use:

          Invoke-AzVMRunCommand -ResourceGroupName 'AXIOMQUANT-RG' -VMName 'AxiomQuant-Build' -CommandId 'RemoveRunCommandWindowsExtension'
     

   • This is a troubleshooting action, not a documented fix for a stuck Managed Run Command resource in Deleting.

Based on the described symptoms, the most accurate conclusion is: if AxiomQuantRepoLocal cannot be removed by Remove-AzVMRunCommand, CLI delete, or REST delete, and instance view shows no active execution, this points to a stale Managed Run Command operation that likely requires backend ARM/Compute cleanup or cancellation of the stuck operation.

References:

• Run scripts in your Windows VM by using managed Run Commands
• Run scripts in your Windows VM by using action Run Commands
• Troubleshoot Run Command
• az vm run-command delete
• RunCommand stuck in cancelling state - Microsoft Q&A