Don't mix the Manage Your Kindle and the Your Media Library pages, odd things might happen
I experienced the like with the old version of the user manual, turned out I had deleted it in the Media Library.
To check: got to amazon.com -> Your Account
Somewhere in the middle there's the Digital Content section.
Click "Your Media Library" column the Your Collections link
Navigate to Your Collections (the second from 3 Buttons on the top)
Just underneath, select View "Trash"
As you described your problem, your issue might indeed be trashed there!
If so, tick the Checkbox and then "perform action -> Return to your Collection
No go to the amazon - Your Account Page again, and navigate to Manage your Kindle (via Kindle Storefront, or via Digital Content Section as described above).
Your Issue should now be listed under "Your Orders".
If yes, click the little Plus sign, and then the "Delete this title" Button.
If no, you might try contacting customer support to help you (contact form is on the kindle help pages)
Viele Grüße.
Pascal