What version of Endnote are you using? With X5 and I X4, you can compare duplicates and copy and paste most fields from one to the other, but not auto “merge” in the same way you can in the X5 update record facility. If Endnote doesn’t see them as duplicates, you can adjust your duplicate search to less stringent in the preferences (like only check Authors or only check title or some criteria that they are the same in) and then you can copy paste from each other.
Othewise you can try to update the one that you like best from the X5 update facility (from a current database) and then delete the other.