Thank you for posting this in Microsoft Q&A.
I understand you want to keep passkeys stored on FIDO2 security keys and delete phone choice from the sign-in options .
If you are enabled FIDO2 as sign-in method and enforced, it with CA policies for a pilot group. You can get iPhone, iPad or Android device, Linked device, Security key. You can also choose to use a passkey from one of the above locations. Unfortunately, there is no way to delete phone choice from the sign-in options.
Please refer this document: https://learn.microsoft.com/en-us/windows/security/identity-protection/passkeys/?tabs=windows#user-experiences
To remove a passkey associated with a user account, delete the key from the user’s authentication methods.: Delete a passkey
Hope this helps. Do let us know if you any further queries.
Thanks,
Navya.
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