@David C I'm glad that you were able to resolve your issue and thank you for posting your solution so that others experiencing the same thing can easily reference this! Since the Microsoft Q&A community has a policy that "The question author cannot accept their own answer. They can only accept answers by others Opens in new window or tab", I'll repost your solution in case you'd like to "Accept Opens in new window or tab" the answer.
Issue: We have MFA in our main tenant, call it Directory X, and we also have a B2C directory that is accessed from our main tenant, but is in its own directory (call it Directory Y). When I log into our main tenant, I get asked for an MFA code, and I use a profile in the Authenticator app for Directory X. From the Directory X azure portal, I go to the Azure AD B2C resource, and from their click over to Azure AD B2C in Directory Y. During the process of going to directory Y, I get prompted for MFA again, and I use a profile in Authenticator specific to Directory Y for that.
I recently changed phones. Re-setting up MFA for Directory X was very straight forward, I went to Account settings and Security Info, and adding a new sign-in method, which provided (or actually updated, taking away the red warning) my Directory X profile that was brought over from the old phone. Again, that profile does not work when I try to access Directory Y. I used my old phone to MFA into Directory Y. From there, I went to account settings,and then Security Info, but when going there, it takes me back to my Directory X settings (and my Directory Y MFA methods are not listed there). How do I get to my Directory Y security settings to update my sign-in methods?
Solution: Resolved by @David C figured it out after some research. You do go to the Security Info page for the user, and then in the upper right, there is a tenant/org toggle that is shaped like three computers networked together. Clicking that brings up the tenant/org picker. All I needed to do was pick the B2C tenant there, then go back onto the Security Info page, and now the authentication methods had the context for that tenant. Hopefully this will help others that have run into the same issue.
If you have any other questions or are still running into more issues, please let me know.
Thank you again for your time and patience throughout this issue.
Please remember to "Accept Answer" if any answer/reply helped, so that others in the community facing similar issues can easily find the solution.