I did a quick search, but didn’t see a good answer for this. I work at an academic institution, and we put out a quarterly newsletter that lists our faculty’s publications. We have over 150 faculty in our department, so performing EndNote searches one at a time is tedious and time-consuming. I have an advanced SCOPUS alert set up that performs this search fine, but EndNote always finds pubs that Scopus does not, and vice-versa. I know this is possible through MyNCBI, but only for individual authors (unless someone knows differently?). Getting over 50+ email notifications each month is obnoxious, and extracting citations from each email is equally obnoxious.
And similarly, search pubmed in Endnote, you can search for Author Affiliation contains your department and then use the “entered between” dates. At the end, if there is overlap between items already in your library and those you pull, I always download the new search to a new temporary library and import that into (with discard duplicates on) the main library, but you may end up keeping the old version rather than the new version, although you can always use the update records feature to get around that.