If you are storing the attachments within the PDF itself (embedded attachments) then you must submit as PDF to preserve them. If you utilize the Workspace attachments tab then you can get around this as the attachments can be stored in a list variable for you from which you can do whatever you'd like!
Feel free to shoot me an email and we I'll explain in greater detail or answer any questions you may have.
After I had already converted my entire workflow to deal with PDF, I realized I probably could have Base64 encoded the attachments and put them into the data model. I was able to do that and submit. What did not work was restoring them client side. The function needed requires privileges granted. It could be done in the map though. I just dropped it since I already had it working another way. I find it a pain to deal with the PDF on the back end which is why I would have preferred that I went the other route.