You can't manage or remove objects that were synchronized through the Azure Active Directory Sync tool

For Cause 1: You want to manage objects in Office 365, Azure, or Intune and you no longer want to use directory synchronization. 

1. Install the Azure Active Directory Module for Windows PowerShell. For more info, go to the following Microsoft website: 
   Manage Azure AD using Windows PowerShell
2. Connect to Azure AD by using Windows PowerShell. For more info about how to do this, go to the following Microsoft website:
   Connect to Azure AD
3. Disable directory synchronization. To do this, type the following cmdlet, and then press Enter:

   Set-MsolDirSyncEnabled –EnableDirSync $false 

4. Check that directory synchronization was fully disabled by using the Windows PowerShell. To do this, run the following cmdlet periodically:

   (Get-MSOLCompanyInformation).DirectorySynchronizationEnabled 

   This cmdlet will return True or False. Continue to run this cmdlet periodically until it returns False, and then go to the next step.
   
   Note It may take 72 hours for deactivation to be completed. The time depends on the number of objects that are in your cloud service subscription account.
   
5. Try to update an object by using Windows PowerShell or by using the cloud service portal.

Note

• Step 4 may take a while to be completed. There is a process in the cloud service environment that computes attribute values. The process must be completed before the objects can be changed by using Windows PowerShell or by using the cloud service portal.

For Cause 2: You delete an object from an on-premises AD DS. However, the object isn't deleted from your cloud service subscription account.

Force directory synchronization by using the steps on the following Microsoft website:

• If some updates and deletions are propagated, but some deletions aren't synchronized to the cloud service, perform typical directory synchronization troubleshooting procedures.
• If all updates and deletions aren't synchronized to the cloud service, contact Support.

Note As an alternative resolution for this scenario, an object can be manually deleted in the cloud service. However, the object can't be updated in the cloud service. For more information about how to resolve this issue, see the following Microsoft Knowledge Base article: