Like a few other people, I occaionally (very occasionally) receive encrypted emails. So far that was not a big deal, because mutt can automatically decrypt these emails, and also search in encrypted emails (by decrypting them first). However I plan to change my email setup in the near future, and allow other programs (like Thunderbird or a mobile client) access as well. This does not work well if the emails are still encrypted. Besides, the emails reside on an encrypted filesystem, there is no need for another layer of encryption on disk.
mutt comes with a command to save encrypted emails as plain emails, thus removing the encryption. However that only seems to work if the encrypted part is a proper mime encapsuled part of the email, not if the encrypted email is just inlined. mutt can decrypt and read the inlined part, but the save command will not remove the encryption. Luckily in 2016 most people get it right and don't use inline encryption.
The "save" command in question is: decrypt-save, and you can bind it to a key. This is my setup:
set fcc_clear=yes bind index A decrypt-save bind pager A decrypt-save
As you can see, I use the uppercase A key here - but it's up to you to find a free key in your own setup. Binding this command to "index" and "pager" allows you to save the decrypted email both from the email view as well as from the mail index - and possibly apply it to multiple commands, using the tagging functionality.