Sorry, said wrong thing. I have never used Word 2016 built in word citation manager, but instead of Export traveling Library from the word document, you export word Citations (from the endnote tab/ribbon in word), but do so to a new library, so you can import just the unique ones into your main Endnote library.
After exporting to the new library, – you open your main library (and you can make a copy first, in case something goes wrong) File>import, endnote library, “discard duplicates” or “import into duplicates library” (not all). It should be able to view any newly imported records, from the recently added temporary group created, if it doesn’t automatically display them.