How do you envision the upload working? Are they going to continue to send email messages and you want Windchill to process those into discussion threads? Why not just direct users to use discussion threads instead of email? This way they do not need to upload, its direct. Or are the external users the problem since they might not be inside of Windchill, right? Transforming a message into a threaded conversation should not be difficult. I have done this in my system. Your trick will be the mechanism to upload it or listen for emails.
If you had a "Windchill service account" with an email, listening for emails (custom client), it could receive forwarded or cc'd emails for processing. Very tricky and I can see the logic getting complicated to map in conversations and extract a thread.
Or you can have a page that takes in an uploaded email file where a user saves off the thread to a file, then goes to Windchill, uploads it and the code transforms it to a conversation. The trick in both cases is dealing with redundant messages, images, etc.
