Last year I did some work in the enterprise/e3 branch to allow a user to store encrypted messages decrypted in another folder.

The patches related to this are:
387e06c7b88bb7f9b1fb86d6123283e5ec6d8ba9
e756d3b6fb04f9497bec341bfc616486faef4f41
4b9b3f0b0e5657460413828d07aa5c77bb722a8f
7ce9f0dc6289f3ec6529e334930dfeef442ff4e3
5ed2e168aafb98807fe10a159b0aff06cea84354
8eb8fc7900a9cfec980e37b19534771bd304fd0f
b9459a4b08ef330aaa3b49a16ac6d9943ad972fa

This is actually a much requested feature. Enigmail even had a funding drive for functionality like this.

I'll probably port these patches at some point but it would be great if someone would pick them up. Basically everything is in place it just needs some actions.