yeah, some fields in that work, and some don’t apply to merging. Recently another user was able to see a difference based on the duplicate preferences, so I thought maybe the developers changed it. This is the help in Endnote on these two settings. I think that the duplicate settings do matter if they are selected or not selected, but maybe only for those highlighted (my emphasis) in the below.
Merge Duplicates in Bibliography
When you select this option, EndNote automatically omits duplicate references from a bibliography. Use this option if you are citing references from multiple EndNote libraries in one paper. In this situation, the same article reference might appear in two libraries and would have two different record numbers. EndNote will not identify the records as duplicates unless you have this option set to merge duplicates.
When you select this option, EndNote checks the bibliography for duplicate references during the formatting process. If duplicates are found, they are removed. References are considered duplicates if they are the same reference type (such as Journal Article or Book) and the following fields are identical: Author, Year, Title, Secondary Title (Journal, Newspaper, Magazine, Book Title, Series Title, Conference Name, and so on), Volume, Issue, and Pages.
Note: The Duplicates Preferences settings do not apply to this feature. The criteria for determining duplicates is fixed for the “Merge Duplicates in Bibliography” setting.