Similarly to how the Subscriptions apply only the current Primary Email, the Bounce Reason needs to apply to the current Primary Email.
We use the Bounce Reason to enroll contacts in a workflow to do several CRM management things. However, if that Bounce Reason applies to a secondary email we get erroneous enrollments. We have switched the Primary Email at the clients request. Changing the Primary Email should clear the Bounce Reason because that reason does not apply to the Primary Email.