Clearing Apple Mail reminders - but email cannot be archived

After right-clicking and clearing the email reminder, the email will NOT disappear from your inbox and go into the archive. For some reason, this doesn't happen until a random point in time later (maybe it has something to do with the Apple Mail cache?).

My inbox is filling with old reminders - that I would love to archive, but I am unable to.

Even as time goes on (thinking it will automatically be cleared) these emails haunt me