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Install the plugin "Find Duplicates".
It has a pull down menu. The second choice is find library duplicates. If you are running it from the library you want to merge to the main library you will then choose your main library as the library to compare to.
I usually run it a few times using first binary duplicates for the exact duplicate. These will be easy to select and exclude from the merge as they are EXACTLY the same.
What will not be found are those epubs that have had bookmarks put in them or changes made with Edit Book or Modify ePub.
The second set of find duplicates I do is to find exact title, author. These you can decide for yourself if you want to merge them or if you want to put a tag or add an update column to indicate which came from the merge.
I use a custom "Update" column and indicate the duplicates.
I usually run Find Duplicates after doing the merge too.
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