Why do comments in comments list disappear when file is saved after a signature is added?

When working with a workpaper file we are using sticky notes, highlight, adding text to annotate a file. Then later we go back and add "place initials" by things that we verify either have been done or the workpapers support that statement. Upon saving the file before adding the initials the file name is XXXX.pdf and the 110 comments I've made in the file are listed in the comments list. Then when I add my initals the file name changes to XXXX-signed.pdf and the 110 comments I've made are still present, but not viewable in the comments list nor when I click on the sticky note is the information in the note viewable. Why would this information disappear?  How do I get it back?
If there is no fix for this Adobe...this is a great reason for my bosses to decide not to spend the thousands of dollars it's going to cost us to buy and implement your software throughout our firm.  We need to retain the comments on a workpaper file as well as be able to inital and sign our workpapers. Many people work in a single workflle and putting our intials next to an item tells the reviewer that not only did we see the comment from the client, but we also double checked to make sure the inforamtion was input into the system and included in the workpapers farther back in the file.
Any help from the user community would be apreciated.
Tanya

I replied to this with a hacky solution over at Stack Overflow: http://tinyurl.com/ybwjfeg
I would prefer that this is resolved via a bug fix, because it certainly appears to be a bug.

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