How to merge two or more Safari Bookmarks.plist files together?
Neither macOS or Safari provide a direct way to merge multiple Bookmarks.plist files so as not to contain duplicate items.

Some choices are:


Manually import each Bookmarks.plist file (Safari > File > Import Bookmarks...) and then manually arrange and reorganize while manually deleting duplicates. 
Use a third-party utility to manage the Bookmarks.plist files so as to utilize any tools the third-party utility provides to remove duplicate items.


BookmarkApp: sort &amp; delete duplicate bookmarks


Developer Website
Mac App Store Preview

URL Manager Pro : the bookmark manager


Developer Website
Mac App Store Preview

Safari Extensions - Search for: bookmarks - At the time of this search it contained "69 results found for 'bookmark'", and some may have the capacity to remove duplicates.
Google, or other Search Engine, for other third-party utilities to manage Bookmarks.

Write your own utility to manage Safari Bookmarks to remove all duplicates from a set of combined Bookmarks.plist files.


Note: I am not affiliated with, nor have used the utilities mentioned herein.