remove duplicates / how will this effect my word-manuscript using that duplicate?

Dear all

The question might have been asked before, but I was unable to find it.

I might want to clean up my endnote library; making folders etcetera. I will probably start with removing the duplicates. However, I am finishing my phd and I do have to edit some of my manuscripts to become chapters in my book. I’d rather not want references in word to be deleted when I change output style or so. What will happen?

For example I have Griswold 2010 placed in two endnote folders, the same reference has #345 and #501 (i.e.). What if I merge them / remove duplicates so that only #345 stays in my library, but in a certain manuscript I used #501

Thank you

Rosa