I have spent hours diagnosing and fixing this issues in a 60 seat environment. There is a lot of missing information in the Microsoft Guides around this . The Hybrid Join configuration appears to be quite buggy and prone to all kinds of potential mishaps. In my case the dual state was preventing the Intune Update process from reporting properly on the devices. Devices that have a state of Hybrid Join and MDM - Microsoft Intune against the same device worked OK. Devices that had duplicate entries with Azure AD Registered - MDM Microsoft Intune and another entry Hybrid Join - MDM - blank do not report correctly in Intune.
In my case the issue was the settings for Azure AD connect.( I needed to turn on Password hash sync ) and the fact that I had a local domain on server xxx.local not a routable domain. The overall steps were as follows:
1. Rerun Azure AD Connect with Password Hash Sync.
https://learn.microsoft.com/en-us/azure/active-directory/devices/howto-hybrid-azure-ad-join
2. Turn on Group Policy for Automatic Enrollment
3. Prepare a non routable Domain for Directory Synchronisation
Using Step 2:- Change the UPN suffix for existing users
4. Delete the device from Azure Active Directory and on the device run dsregcmd /debug /leave – reboot device .
https://learn.microsoft.com/en-us/azure/active-directory/devices/faq
Section “ I disabled or deleted my device in the Azure portal or by using Windows PowerShell. But the local state on the device says it's still registered. What should I do? “
5. On the device Connect to your Workplace
Settings – Accounts – Work or School Connect. I performed this step even though the Automatic enrolment should perform this step. Perhaps Microsoft can give some guidance as to whether this step is required.
Showed up as Hybrid Joined. Logged on to the machine Accounts – Work or School – signed in - allow your organisation to manage the device -yes came good.
It should look like this
After this process it may look like this
The Windows process on the PC will clean this up and convert to one device entry. Starting from Windows 10 1803 (with KB4489894 applied), dual state being removed automatically from the device itself.
It is also possible that an entry Azure AD registered with MDM State Microsoft Intune will also show up. This state should also be rectified automatically on devices Windows 10 1803 and above.
6. Checks
Use the dsregcmd /status command to check the status on the machine.
Sometimes it is necessary to wait till the automatic enrolment process kicks in and this may require rebooting a few times.
__7. Errors.
__
Even when following these steps the success rate was about 50% first go. Sometimes it was necessary to cycle through the steps of deleting the device in Azure AD, Running the command dsregcmd /debug /leave command and rebooting a few times. Sometimes the status on the machine using the dsregcmd /status showed all OK and successful but the information in Azure AD devices sometimes contradicted the machine state even after leaving some time for the Azure portal to update. It is also taking some days for the correct status of the device in Azure AD to show a successful outcome in the Intune Update reporting>
You will also quite often get this error in dsregcmd /status
Previous Registration : 2023-03-25 22:30:45.000 UTC
Registration Type : sync
Error Phase : join
Client ErrorCode : 0x801c03f3
Server ErrorCode : invalid_request
Server ErrorSubCode : error_missing_device
Server Operation : DeviceRenew
Server Message : The device object by the given id (795092fd-66a7-4bb8-82c6-c45edcs4565ds3456) is not found.
Https Status : 400
Request Id : 1f017a77-962e-4cd2-b731-33c1443ba588
Executing Account Name : DNB\Steve, steve@dnbfakeemail.com.
This usually fixed itself after a reboot or two