Azure migrate discovery shows "Discovery Incomplete" for Windows servers after "Validation successful"

As you mentioned both appliances report identical diagnostic errors, the functional impact is different:

• Linux discovery succeeds
• Windows discovery fails

This indicates that the diagnostic errors themselves are not the root cause, but merely generic appliance health warnings. The real issue is specific to Windows discovery on the appliance, not to outbound connectivity or firewall configuration.

The diagnostics check validates:

• Appliance service restart behavior
• Reachability of Azure Migrate endpoints

These checks are generic and apply equally to Linux and Windows discovery, Minor HTTP 400 / 404 responses do not fully block discovery. Therefore, both appliances legitimately report the same warnings.

Why Linux discovery still works

• Linux discovery relies only on:
  • SSH (TCP 22)
    • No CIM / WMI / DCOM dependencies
    • As long as SSH works, Linux machines can be discovered successfully

Why Windows discovery fails

• Windows discovery requires CIM/WMI libraries on the appliance
• The error shown:

System.IO.FileNotFoundException
Microsoft.Management.Infrastructure

indicates that the CIM/WMI runtime dependency on the appliance cannot be loaded

• Without this component:
  • Windows metadata collection fails
  • Validation cannot complete
  • Servers remain in “Discovery Incomplete” state

This is why the portal explicitly states that the issue does not indicate a problem with the target guest VM.

Confirm Appliance Service State:

1. Log in to the Azure Migrate Appliance VM.
2. Open Azure Migrate Appliance Configuration Manager.
3. Navigate to Manage services.
4. Select Refresh appliance services.
5. Wait until all appliance services restart successfully.
6. Re-run discovery from the Azure portal.

This step ensures the Azure Migrate discovery and management services are running properly and can resolve temporary runtime issues.

Confirm the Issue Is Appliance-Side:

Based on the validation already performed:

• WinRM connectivity (TCP 5985) is functioning
• Credentials are valid and have administrator privileges
• Required outbound URLs are reachable
• Network connectivity between the appliance and servers is working

These checks eliminate target VM configuration and network connectivity as the root cause.

This indicates the failure is occurring within the appliance runtime environment.

Redeploy the Appliance (Microsoft Recommended Action):

If the appliance reports errors such as missing Microsoft.ManagementInfrastructure or similar CIM/WMI dependencies, the supported remediation is to redeploy the Azure Migrate appliance.

Recommended steps:

1. Deploy a new Azure Migrate appliance using the latest appliance package (OVA/VHD).
2. Do not clone, snapshot, or reuse existing appliance VMs.
3. Avoid performing OS hardening or manual configuration changes before the appliance setup and discovery are completed.
4. Register the new appliance with the Azure Migrate project.
5. Re-add the Windows servers for discovery.

Manual repair or replacement of CIM/WMI (Microsoft Management Infrastructure) assemblies inside the appliance is not supported, because the Azure Migrate appliance is delivered as a managed and preconfigured runtime environment.

Therefore, redeploying the appliance is the supported and recommended resolution when these core components are missing or corrupted.

For Windows servers that validate successfully but show “Discovery incomplete,” focus on the ongoing discovery and software‑inventory path between the Azure Migrate appliance and those machines.

1. Confirm discovery timing

• It can take up to ~15 minutes per vCenter source, a couple of minutes per Hyper‑V host, and 1 minute per physical server for initial discovery to complete.
• Changes in discovered server configuration can take up to 30 minutes to appear in the portal, and software inventory can take a few hours.
• If the state remains “Discovery incomplete” beyond these windows, continue with the steps below.

2. Refresh the appliance services from the portal After waiting the above intervals:
3. In Windows, Linux, and SQL Servers > Azure Migrate: Discovery and assessment, select Overview.
4. Under Manage, select Appliances.
5. Select Refresh services and wait for the refresh to complete.
6. Recheck the discovery status for the Windows servers.
7. Verify connectivity and prerequisites from the appliance to Windows servers Even though TCP 5985 is open and credentials validate, software inventory and deeper discovery can still fail if prerequisites are not fully met:

• Ensure all Windows servers meet the Azure Migrate physical/VM prerequisites and port access requirements (WinRM over HTTP 5985 must be reachable end‑to‑end, and any proxy/firewall between the appliance and servers must allow it).
• On the appliance, add the IP addresses of the Windows servers to the WinRM TrustedHosts list and retry discovery. This is required to allow remote inbound connections on port 5985.
• Confirm the correct authentication method is selected on the appliance for these Windows servers.

If connectivity or prerequisites are not met, you may see software‑inventory errors such as:

• 60001 – UnableToConnectToPhysicalServer: indicates network or prerequisite issues. Resolve by ensuring prerequisites and ports are open and TrustedHosts is configured, then retry.
• 60002 – InvalidServerCredentials: indicates expired/incorrect credentials. Edit the credentials on the appliance, revalidate, and then refresh services.

4. Check for software‑inventory specific errors If discovery is incomplete specifically because software inventory or guest operations cannot run, check the error codes in the Azure Migrate portal for the affected Windows servers. Common causes include:

• Missing or invalid guest credentials (10004, 10005).
• Unsupported OS type (10006 – only Windows and Linux are supported).
• WMI/PowerShell or environment issues on the guest (9022 Get‑WmiObject access denied, 9023/%SystemRoot% empty, 9024/%TEMP% empty, 9025 PowerShell corrupted).
• VMware guest operations issues (if applicable) such as missing/outdated VMware Tools (9016, 9021) or missing guest operations privileges on the vCenter account (9015).

For each error, follow the specific remediation in the software‑inventory error table (for example, granting WMI permissions, fixing environment variables, reinstalling PowerShell, or updating VMware Tools), then revalidate and refresh services.

5. When to contact Microsoft support If:

• Discovery remains “Incomplete” after verifying connectivity, credentials, prerequisites, and refreshing services, or
• You see transient internal errors (for example, 10002, 9012, 9017) that do not resolve within the next 24‑hour cycle,

collect the appliance machine ID (shown in the footer of the appliance configuration manager) and open a Microsoft support case as recommended in the troubleshooting guidance.

References:

• Troubleshoot ongoing server discovery, software inventory, and SQL and web apps discovery
• Tutorial: Discover AWS instances with Azure Migrate
• Tutorial: Discover Google Cloud Platform (GCP) instances with Azure Migrate