Hi Greg,
I'm not sure to understand well your problem.
You have an AD with a local non-routable domain (as domain.local), where you have changed all UPN for users having UPN=MainEMAIL synchronized and used on Office 365. So That is perfect. Where is the conflict?
As UPN=PrimarySMTPAdddress, why do you want to replace UPN by Email for login in ADConnect? Ideally, they should always be identicals.
It is sure that changing actual correct UPN in AD will have a bad impact on your ADConnect synchronization and users authentication.
Modifying ADConnect only to use Email in place of UPN is not a good choice.
Perhaps have you missed to indicate us some important information that request a specific change!
Regards,