API stopped querying by metadata

I might have missed something, but from that comments you’re describing an issue with authentication and not user search. By default, to my knowledge the authentication pipeline does not require user search so the user search restrictions should not matter. Do you have custom rules that depend on user search? If that’s the case, which is not recommended, then please use that email address I mentioned to expose the situation; you can leave a note here mentioning that you sent the email so I can take a look and ensure the case is reviewed.