Question about Endnote when combining several parts together into one article

I have written several chapters seperately, using Endnote to add reference when writing. Now it is the time to combine these chapters together and I found problem with the Endnote references. They adds chapter to chapter, which makes the reference disorder, and some of them are duplicated several times because I refer it in different chapters.

How to deal with the problem?

Which version of Endnote are you using, and which style.  Attach the style to your reply please.

I am using Endnote 9.0 and I am using Chicago 15th B. Eg. as

Arce, I. (2003). “The weakest link revisited.” Security & Privacy, IEEE 1(2): 72-76.

Try unformatting and reformating the complete document. You may have delete individual bibliographies, but the best way to combine them, would be to unformat the individual chapter documents first and then combine and then format.  It should create one reference list at the end, with no duplications.  Remember that if you unformat a document, you must re-engage the CWYW function while you are refomating, (third tab).