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To upload an X.509 certificate in FlexDeploy, navigate to the Credentials screen and select the option to upload a certificate. You will need to use a Certificate-type credential to store the X.509 certificate and an a PRIVATE_KEY (was called SSH-Key prior to 9.0.0.3) type credential to hold the private key that corresponds to the certificate. Ensure that the private key matches the uploaded X.509 certificate to enable proper functionality.
If you are using a shared mail box, make sure to also grant the FlexDeploy user access to this mailbox using the Microsoft Admin center.
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Configure FlexDeploy to use the new application
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Navigate to System Settings → Email Settings and use the page Configuring Graph OAuth - Microsoft Office 365 Email with Graph API to configure it.