Hi @Ben J •
Thank you for sharing your issue on Microsoft Q&A.
I understand that You are working with a client migrating to Microsoft Intune and using Microsoft Authenticator for MFA token backup and restore during device upgrades. The Azure AD "Additional Security Verification" page has been removed due to the transition to Microsoft Entra ID.
Users cannot modify MFA methods because they can't access the Security Info page without logging in first.
After testing MFA setup by deleting and restoring the Authenticator app, your account was locked and required approval from the deleted app. You tried using "Require re-register MFA" and per-user MFA re-enrollment, but one had no effect, and the other disabled MFA, marking your account as MFA-disabled. Despite Conditional Access enforcing MFA, no re-registration prompt appeared during login.
Backup and restore work only on the same device type (iOS to iOS, Android to Android). On iOS, the backup feature uses iCloud but requires linking a personal Microsoft account to the Authenticator app.
To resolve the issue, follow these steps:
As you are facing issues with your current setup, removing your account from the Authenticator app can help reset its state.
Use the Intune or Azure AD admin center to push MFA re-registration for users. This can help ensure that they are prompted correctly during their next login attempt.
As an administrator, revoking active sessions can force you to re-authenticate, which may prompt MFA setup again.
After revoking sessions, it is required to re-register MFA settings through the admin center to ensure you have valid authentication methods set up.
Once you have successfully re-registered with MFA methods, now you can re-add your account in the Microsoft Authenticator app.
For additional information please refer this links: Back up account credentials in Microsoft Authenticator - Microsoft Support
Use Microsoft Authenticator with Microsoft 365 - Microsoft Support
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Harshitha Eligeti.