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.

Thanks!

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