I have four similar large collections of website files. They are archived copies of a similar directory tree from different times in the past.
I want to merge them all to the most recent collection, archive1. Due to poor www-knowledge 15 years ago, some website trees contain necessarily identical files to work (.css, empty pages, placemarkers etc.). Additionally some files have been corrupted to 0-byte files, and I want to replace those with versions from archive2 upwards.
$ fdupes archive1/ archive2/ archive3/ archive4/ -rNdn
should do mostly the right thing, but will also detect duplicates within archive1 itself.
What is the best way to delete duplicate copies of my files, without deleting the duplicates inside archive1?
PS I'm aware of this question which partly addresses the follow-up issue of copying non-duplicate versions into archive1.