The set of book files I used for my testing were created using "Save to Disk" with the following template pattern "{author_sort:sublist(0,1,&)}/{author_sort:sublist(0,1,&)}~{series}{series_index :0>2s| |}~{title}". Which places books for the same primary author in one sub-directory. And, yes the file set for a book are all named exactly the same (excepting .extension).
But, you keep over-looking the pointer to where there is a problem. Doing adds using the EXACT SAME set of book files ---
Using "Add from directories, ... (One book per directory...)" works as expected. You get correct (from .opf/cover files) metadata/cover.
Using "Add from directories, .... (Multiple books per directory...)" does not. You get incorrect (only from internal book file) metadata/cover.
To get correct (updated) metadata I have to place every book file set in individually separate subdirectories and then "Add... (One book per...) option.
As soon as I get time, I will do some screen captures to show you that one way works and the other way does not work.
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