In general, this problem is really hard to address because the capabilities of clients vary so greatly.
Have tested many clients and its a total mess. For text only emails its not too bad but attachments break things in strange ways. The only ones working correct are outlook and Mail on iOS. Though display is not the most convenient. They both enable reply to original message and thats a great improvement compared to MM2
Perhaps your subscribers would be better off with single-message mode rather than digest mode. I'm not really clear on why anybody subscribes in digest mode any more. Digests still make sense for individual collections of messages, eg, "Your Honor, here are all the emails in which the defendent libeled my client." But for an ongoing stream such as a mailing list, I would think you would be much better off to receive the individual messages and let your modern client do its own thing with grouping threads and folders, and threading and ordering posts. Obviously, people like their own ways of doing things, but that suggestion might be useful for some of your subscribers. I hate to ask you to ask your subscribers to learn how to use their clients, as that frequently doesn't go over well, and they'll probably ask you to teach them with a client you've never used yourself :-/.
yes, yes, yes full ack. Thats what I am doing. But its extremely hard to convince users to change what they have done for a long time.
However, if that's an option, most email clients provide a way to "burst" the digest into individual messages, which will then be threaded in the normal way for that client. This provides the user with the "download all the recent messages periodically" benefits of the digest, as well as the threading capability of the client.
Can you list clients that can do that? I’d like to have options to recommend if users insist on digest.