Not rare, I have seen this multiple times in two organizations I have managed.
Here is a current fix: sign in to Entra, Navigate to Users, select Per User MFA in the top menu (may be behind asterisks); select user in MFA list and then select User MFA settings from top menu. Select "require selected user to provide contact methods again. Save. Delete and reinstall the app. The QR code will now appear when that user tries to login and it will prompt as if the first time.
It was rare in these forums before this thread LOWY Admin, and everyone using a Work and School account is in the wrong forums, since these forums are Community volunteer support for consumer users of Microsoft Personal accounts., which is why this thread so quickly became confusing. But then, obviously no one knows that the Microsoft Learn - Q&A forums actually exist, especially those in small organizations using Azure, so that created the initial problem for those.
The complications here exist because Microsoft had merged the older authenticator product they initially used with the Azure - Work and School accounts with the Microsoft Authenticator app used for Personal accounts a few years ago, likely to solve support and basic operational problems with the 2 different apps. But as a side effect, created the mass confusion you've seen displayed in this thread.
Supposedly the only place you can officially get aid with the Microsoft Authenticator is a sub-forum of those Learn - Q&A forums, but since I've actually been using the authenticator with a Personal account for several years, I've tried to provide what limited support I can for Personal accounts here, since if you go review that forum, it's at least as confusing to navigate as this thread if not worse.
It eventually became apparent that the deeper problem here was always related to either a lost, stolen or damaged phone or in rare cases possibly a corrupted Microsoft Authenticator installation.
Actually, you've pointed out another complication that occurred while this thread has existed, since the migration from various earlier authentication apps or systems to the newer Entra you've mentioned in your post is relatively recent, so that migration has likely made the management of these issues even more confusing for Admins, especially those supporting small business(es)
Since I don't personally have a Work or School account, I have no direct experience with those and could only use what I either found in Microsoft support documents or specific details from a few postings in this thread. Your post is quite helpful, but since we don't truly know whether everyone with a Work or School account has actually been migrated to Entra yet, making any blanket statement about this is dangerous at present.
Hopefully you now understand the issues I was up against when this thread began, and why it's such a mess, since I've had really no support from Microsoft to try and resolve the issues created by the brief history I've detailed above. In fact, if you find any threads in these forums about the Microsoft Authenticator, you'll see that if a Microsoft tagged individual gets to it first, they've been specifically instructed to redirect them to the Q&A Forums for the authenticator.
Rob