Pasting one document with references into another

@klbesemer wrote:

Does anyone perhaps know a way to reintegrate the separate bibliographies without unformatting and reformatting the entire document?

This might be less methodical than Leanne’s approach but it would allow bypassing unformatting/reformatting. 

This method assumes you’ve first added the EndNote reference records from the “new” chapter into the main EndNote library.  Next, check that the  “Enable Instant Formatting on new Word documents”, “scan for temporary citations”, and “Check for citation changes” options are activated (TOOLS, CITE WHILE YOU WRITE, CITE WHILE YOU WRITE PREFERENCES). Then simply copy-and-paste the new chapter text (omit the references) into the book-document.  The instant formatting and citations functions will compare the citations from the new chapter against the main EndNote library and should update the  book’s bibliography.

This worked for X3 but suggest you run a small test, combining a section from two different chapters and check the resulting bibliography.