Microsoft Authenticator Issue - Hasn't transferred Two Step Authentication Accounts

Question

I recently had to get a new phone due damaging my previous one, and having recently re-installed Authenticator it hasn't transferred my accounts I use for authentication. It's the same email and Microsoft account, however.

I can't re-authenticate my previous accounts, due to their process of not letting me log in without authentication first and using the codes, which I can't access because they did not transfer.

Advice would be greatly appreciated, thank you.

PS -Wasn't sure what category to place it under, I apologise if it's wrong.