You cannot control how customers send email to your support mailbox. When you receive emails encrypted with S/Mime, they do not get tracked into Dynamics. This is a huge problem, because customers get upset when their emails do not get answered. With thousands of incoming emails every day, it is easy to miss messages that do not get tracked. It makes it additionally difficult when some messages that are tracked into Dynamics do not get tagged with 'Tracked to Dynamics' in the support mailbox because they were marked in another mailbox (that's another issue).

Unfortunately, Office 365 does not have a way to set up a rule to forward these or flag them based on the fact that they are encrypted, but since a human can see that this message is not able to be processed by Dynamics, maybe there is some way to do it with a computer.

The answer I got from the Dynamics team: "It as not an issue with Dynamics Constraint. We can only recieve[sic] the email what Exchange provides us. As stated in article [https://support.microsoft.com/en-us/help/4490718/email-fail-to-synchronize-to-dynamics-365-when-encoded-with-pec], neither Rest or EWS (which dynamics uses to sync emails ) provide support for callers to recieve this encrypted emails." Since the email and Dynamics are both provided by Microsoft, I'd like to think there are enough brains there to work this out.