If we're talking thousands and in many folders, I would put this client into CSKM and keep private key on his machine, or SKM and move his private key to the server, his email should still be able to be decrypted, just at the server instead of the client (if in SKM)
But if its just a few hundred, I think you can bulk decrypt via the PGP viewer, just select multiple emails and drag them all onto the viewer at the same time, and itll process them in-turn.