You cannot use the configuration manager console to manage mobile devices for this subscription because the mobile device management authority has been permanently set to Windows Intune. Select a different Windows Intune subscription.

You may have got this message when you were trying to set the Windows Intune Subscription in SCCM : 

Wonder Why you are getting this ??

SCCM throws the message when it looks to the Intune Subscription & finds out the Mobile Device Management Authority in the subscription is set to "Microsoft Intune" 

Now, the worst thing is, there's no GUI method to reset this setting in Intune to "Managed by Configuration Manager".

The only way to reset this setting is to call Microsoft Technical Support & ask them to change the setting to default & then you again reconfigure the setting to CM.

MS Support can be contacted on 8006427676.

The MS Technician's can also ask you to :-

1. Retire all Modern Devices (mobile devices) from within the Microsoft Intune Admin Console.  It is important that you do not attempt to retire a device from the device itself for this procedure to be executed.  

2. Delete the Service To Service Connector (under Administration > Mobile Device Management > Microsoft Exchange).
Or Disable the Exchange Connector if you have set that up.

3. Remove any and all side-loading keys and code-signing certificates from the Microsoft Intune Admin Console.

4. Delete the iOS APNs certificate in Administration > Mobile Device Management > iOS page.


5. Delete any and all published applications that are for MDM Devices in Software > Managed Software.


Check :

Setting Mobile device management authority to Configuration Manager in Windows Intune