Currently when endnote detects a duplicate and you are asked to keep one, the one you do not keep is deleted. That is, it is removed from groups it was in, and becomes a broken link in documents. This is unintuitive and non-functional.
Expected and ideal behavior would be for the references to be merged, where any links referring to one of the references now refers to the other (or a new merged reference), and now a single, identical, reference appears in all groups that had either of the two originals.
From what I can tell, this would require Endnote to keep both reference codes in its internal database, but assign a redirect from one to the other, so the user only sees the one.
This should be implemented.