Apologies for the delay in responding.
I would recommend updating the information related to Authentication ( from Federated to Managed ) in the Azure AD Connect. Always prefer to use Azure AD Connect tool to make these changes.
Would suggest to run the wizard in the Azure AD Connect by unchecking the federation option and other options ( keeping default as before ) for authentication ( PHS or PTA ) as per your current requirement and no issues will be seen/reported in Azure AD/or with users while accessing the applications.
If you have any other questions, please let me know.
Thank you for your time and patience throughout this issue.
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