I have spent most of this morning trying to find that needed paper trail the OP mentions. It is very confusing when the originally filed return changes its status and whether or not it displays in EF Center. 

I currently have an amendment that is displaying in EF Center as 1) Federal Extension - Completed/Accepted/E-file Complete and 2) Federal Amendment - Completed/Rejected/Resolve Reject. I see nothing at all about the originally filed return. It was also efiled and it should show up in the EF Center.

If there is a problem with an amendment being rejected, this display of statuses becomes even more confusing. It would be helpful if there was a more consistent treatment of the files. 

It can also be very confusing if the file names aren't exactly right. In my real-life example below, I didn't follow the naming syntax suggested in the instructions (it doesn't make sense to me to name a file COPY when it is the original and has been accepted, inserting ORIGINAL makes more sense to me). But even with that, they are backward. Because I named the originally filed file with ORIGINAL and named the other/old file AMEND, I did the amendment in the wrong file, the one named AMEND. That's my fault but it really created a huge mess that shouldn't have been allowed to happen. There should be a better, more foolproof way, IMO.

Here is a recreation of my HomeBase View for All Tax Returns: