Thanks for your answer Jerome.
In fact my bookmarks are OK on the Mac and in iCloud (the Safari checkbox is active in the Mac's iCloud system prefs). Using Little Snitch, I can see network trafic to iCloud servers when I create a new bookmark on the Mac, and the bad “ghost” bookmarks didn't came back for several weeks now.
The problem I have is when I activate the bookmark sync on the iPhone or the iPad, those devices do send bookmarks to iCloud (then to the Mac also…). But the bookmarks should not be there as I erased them when I unchecked the iCloud sync on both devices and selected "Delete" (as mentionned at step #3 of your complete tutorial, and all the million ones I've check btw). All the bookmarks should have been erased but they are not. On the iPhone or iPad, I can see them when I try to save a new bookmark in Safari.
This is when I click on the bookmarks icon on my iPhone :
And this is when I try to save a new bookmarks on the same iPhone. I can see the folders containing the “ghost” bookmarks :
I would like to erase completely the "ghost" bookmarks from both iPhone/iPad, without having to restore "as new" those devices and loose 5+ years of my digital life and network access for a ¡#%@? bookmark file! (when I restore from a backup, the “ghost” bookmarks are also restored…).
My question should have been more accurate : “Can anyone, having duplicate bookmarks, confirm that the bookmarks are not really erased FROM THE IPHONE/IPAD when unchecking the iCloud bookmark sync ON THE IPHONE/IPAD, and if they are still visible when saving a new bookmark on iPhone/iPad?”
The solution would be to delete the Bookmarks.plist files directly on the iPhone/iPad, or at least in the iPhone/iPad backup files located on the Mac (and then restore the iPhone/iPad from this “cleaned up” backup). But which file to edit/delete?
Thanks for your help