Unable to delete links: "XML structure element, not in layout"

Question

Hello all,
I'm having an issue in InDesign where I'm unable to delete links appearing in multiple files that have even made their way into one of our templates. They do not list a page number where the object appears and clicking on the "< >" does nothing.
A cursory search of the InDesign forum yielded two results, both of which were answered by having the OP go into the document structure and delete stories from the Root (see below). In my document, however, there is NOTHING listed under Root in the structure. Where are these files and how do I get rid of them?
I'd really like to eliminate this problem before it spreads further. Any help?
Matthew
http://forums.adobe.com/message/2641501#2641501
http://forums.adobe.com/message/2450330#2450330

Answer 1

Slight update: In another document the page number is listed as "DT." When I click on it I get this this message:
Links panel:
This document *does* contain elements in the structure but even when removed from the structure the items stay in the links panel. So my questions are:
1) Am I removing items from the structure incorrectly?
2) If I've already removed items from the structure, how do I remove the links that were associated with that content?