Thanks for sharing more context.
This is an expected behavior when using the "Azure AD connect wizard" as well as "PowerShell Msol" cmdlets in combined way (such as convert-msoldomaintofederated
/Set-MsolDomainAuthentication
) for switching between PHS and ADFS because if we use PowerShell cmdlets then Azure AD connect wizard stop managing federation for you.
Let's say ADFS was initially configured and federated via Azure AD Connect, then later switched to PHS (Password Hash Synchronization) from federation via Azure AD Connect, so there is no discrepancy until now, but if you use PowerShell cmdlets like "convert-msoldomaintofederated" to revert back to ADFS federation rather than using sync wizard, then Azure AD Connect unaware of these changes and will continue to use PHS as a backup along with federation.
Screenshot from my environment, you can see that Domain was federated using convert-msoldomaintofederated but Azure AD connect continue to use PHS as backup because earlier it was managed via Azure AD connect.
However, at this stage primary authentication for user sign-in would be ADFS federation but PHS continue to be a backup. You can always Run the customize synchronization options to remove this optional PHS feature as shown below:
So to avoid such instances, try using Azure AD connect wizard to switch between PHS and ADFS not PowerShell in combined way. Here are detailed steps to switch back to federation by using wizard.
To learn more, refer following articles. Hope this was helpful.
Migrate from federation to cloud authentication: https://learn.microsoft.com/en-us/azure/active-directory/hybrid/migrate-from-federation-to-cloud-authentication
Setting up PHS as backup for AD FS in Azure AD Connect: https://learn.microsoft.com/en-us/azure/active-directory/hybrid/tutorial-phs-backup
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