The final cause was determined to be accounts with sandboxes and their crons. Disabling those stopped all duplicated emails and ended the unwanted notifications. A permanent fix for the future is being applied.
Posted 29 days ago. Sep 16, 2019 - 12:33 EDT
The email rule for discontinued medications that created the issue has been disabled on all accounts for the time being and will be reintroduced once the root cause is determined and fixed. As of now all other email notifications should be delivered as expected.