Oh boy, sorry you are having to deal with this. Email is hard!
Has this ever worked for you before or is this a new setup that you are trying that is not working? What email-in method are you using? POP3 or mail-receiver?
Can you explain your setup and process in a little more detail? I am a little confused. I don’t think you can expect to have the replies all associated with the same topic if the email people are replying to did not come from Discourse.
I have a category set up this way on my neighborhood forum as a sort of yahoo group replacement. People can write to that category’s custom incoming email address which creates the topic and gets distributed to everyone watching the category (which by default is everybody). They can also start topics directly on the forum which also get distributed. Any replies by email are associated with the topic that is created, and also get distributed.