Two reference lists?

Hi! Apologies if this query has been raised before…

I am handing in my thesis next week and I have merged various sections into the one final document. Upon doing so I have two reference lists, both in alphabetical order. How do I merge the two? I tried unformating and then updating the references using the endnote MS taskbar but that didn’t work… If I cut and paste each one into the right position will I lose the in-text referencing? I’m using endnote X6 and MS 97-2003

Looking for help! :s