Creating document with 2 bibliographies and multiple section breaks?

I work as a librarian/copy editor for a number of groups that conduct systematic reviews, these reviews when published are submitted to PubMeds ebook database ‘Bookshelf’. Due to the nature of Bookshelf each of these documents must be formatted and styled using strict templates to create properly tagged XML files for uploading, these templates require section breaks at the end of every section in the document.

With that being said I often need to make multiple bibliographies in these documents. Typically one for the main body text and one for the appendices. The in-text citations then need to be linked to their respective bibliographies using CWYW. Unfortunately there seems to be no way to do this in EndNote. I am familiar with editing my output styles in EndNote to add a bibliography after every section break in the document, but I am working in documents with tens of section breaks that only have two bibliographies, so this method will not work. I would be open to changing the current section breaks in the document into page breaks or something, but the required templates for the work I do make the current section breaks mandatory.

I would also be willing to split the document into 2 parts to CWYW them before merging them back together, but the links from in-text citations to their bibliographies are, in my experience, not preserved when merging documents with their own respective bibliographies.

Does anyone have any experience dealing with this problem? Or are there any plans to add this functionality to EndNote?

To reiterate I need to: Make a document with 2 bibliographies, each with their respective in-text citations linked to them, but without using section breaks to do so.

If you merge the two, and make sure CWYW is off, are the links not preserved? 

I googled Word Master Documents hoping that that option had improved, but the general consensus is still – don’t touch them with a barge pole.  

Merging the documents will break the links for at least one of them. Which is too bad. It seems the consensus from online tutorials is that this is currently not possible.

Hopefully this is something in the works for another version or update. I know of a lot of folks who would appreciate this being an option.