Endnote making me see red...

I like Endnote, but it’s giving me a headache with something.
I merged a bunch of documents with separate libraries together, and I thought I did what you were supposed to do: I unformatted the references, merged the libraries, and then reformatted references in the combined document. Now the merged library has no duplicates, but my bibliography is FULL of duplicate entries and I have no idea how to fix it. Any advice?

Check your “Formatting” settings in Endnote program preferences (edit preferences in windows version) to make sure you have merge duplicates on (see image).  Also check your duplicates settings to make sure they aren’t too specific and or have the punctuation settings off. 

If that doesn’t work, Make sure all the old libraries are closed and only the merged library is open.  Make a copy of the manuscript (for safe keeping incase this doesn’t work) and then convert your citations to “unformatted” (NOT plain text) and then  update citations and bibliography (these are options on the endnote ribbon).  This may force you to select the correct citation for many as the record numbering will have changed.  

In future, you should be able to use multiple libraries to format the paper, especially if the duplicate settings are set correctly.