Duplicate references cited in differernt papers

My EndNote X9 library has numerous duplicate references. I would like to clean it up but have no way to tell which record number of a reference was used in which paper. If I pick a method and say, delete the newest version of a refernce, I am worried that I will run into issues down the road. Is there any way to prevent citation problems, or how do I deal with them when they inevitably do arise?

A similar question was asked ~1 year ago by a different user, but no replies were posted. Any advice would be greatly appreciated.


Any existing manuscripts, as long as the paper is not “convert to unformated citations” (curly bracketed) will retain all the information it needs to update citations (in a traveling library, embedded in the field).  Even if you do convert to unformated citations and then update - it might ask you to select the correct record from a limited list including the one you retained to insert and replace it.  

Thank you! I’ll give it a try on a small scale and see how it goes.