In one case, MFA option popped up and disappeared without being able to enter information.
Found this, and registry key seemed to work:
There are a number of reasons for this. First I would look inside the Office 365 admin portal to make sure your password expiration policy is not set to only a few days
If this is ok, setting the below registry key to 1 in below path often resolves it
Path: HKEY_CURRENT_USER\Software\Microsoft\Office\16.0\Common\Identity
Key: DisableADALatopWAMOverride (DWORD)
I would try that on a single user to see if it works before rolling it out. If that doesn't work let us know.