Previously, we had a service account user@domain.edu. This is an e-mail alias that forwards to our development team.
At some point, Atlassian began intercepting logins ending with @domain.edu and sending them to Microsoft's login flow.
So when I try to sign into our user@domain.edu account, it authenticates against Entera ID, where no such account exists because, as stated, this is just an e-mail alias.
Effectively we have been locked out of our account by this change. I don't see a way to continue using our old password based sign-in.