main section of document: cite references as they appear numerically
last section of document: cite new references (not appearing in the main document) and start numbered reference list over at (1). Citations in the last section that already exist in the main section should reference the original number
works cited list: a single works cited list should be at the end of the document that goes from 1 -> N (N = last citation number in main section of document) and 1 -> M ( M = last citation number of new references in last section of document).
Before we put on our thinking caps for this unusual requirement (which I am not sure is solvable): In the last section, how does the reader know if the citation (1) refers to the main citation list or the new citation list?
Are you using EndnoteX3 or an earlier version?
When you are inserting the references in the last section, do YOU know what is a new reference and what has been cited before?
I think you are going to need to do some work at the end of the document. Like reference everything in a single document, then splitting them, and perhaps reformatting the last section, or unlinking and renumbering… The exact strategy will depend on how many references are new in the last section, and how many are cited in the main section. (and how they are distinguished.
Alternatively, perhaps you can use footnoting in the last section, to distinguish the two types of citations?
I’m not entirely sure what you’re saying you want to do, but I think the new capability of EndNote X3 to create section bibliographies might be able to solve this for you. Have you tried it? If so, what’s it doing that’s different from what you need? It sounds like you want to select the third option, to have a bibliography at the end of each section and one at the end of the document.
If you want cites in the last section to keep their numbers from the first section, you really have to continue numbering across the sections. Otherwise you’ll end up with the same number twice in one section, won’t you?
For example, if you cite [1] in the first section, and it’s a paper by Atticus, in the last section [1] would also have to be Atticus. Otherwise there’s no way you could use Atticus again and you say “Citations in the last section that already exist in the main section should reference the original number”.
You can’t both start the numbering over and reference the original numbers, unless I’m not understanding what you want. Can you give more examples?