I just renewed my SMIME email certificate after the previous one expired.
Now any new mail I write in Mail.app simply disappears after I close and reopen Mail.app. They are not deleted (Trash or in Spam), simply no sign of them.
It doesn't matter if I "encrypted", "signed" or not.
Drafts seem to be un-touched. (Until I try to send them)
My Mail.app is set to sync with Gmail servers. And the mail does get delivered to recipients it appears, including to my iPhone which I share the .p12 identity with.
But closing and re-opening Mail deletes anything Sent/Received from/to my email address.
I tried to fix this by deleting the previous expired SMIME Certificate /private key pair, but that did not resolve. I backed up that identity so I could hopefully read that old mail if needed in the future.
EMails received from other accounts seem to not 'disappear'. If I reply to them, naturally my reply disappears.