The BOOKS content.OPF?
The one in The Library folder is the backup of what the GUI shows
One of my Rakutan Kobo books has:
Code:
<meta property="belongs-to-collection" id="id-4">The Draconis Memoria</meta>
<meta refines="#id-4" property="collection-type">series</meta>
<meta refines="#id-4" property="group-position">1</meta>
Calibre embeds (on demand) series
Code:
<meta name="calibre:series" content="Quarters"/>
<meta name="calibre:series_index" content="1.0"/>
USUALLY adding book via the GUI, finds those and fills in the DB entries.
But Calibre has plugins that can 'clear out' non-DC metadata, so it is possible the GUI has Series and the book no longer does.
I don't know how the reverse would happen?

You replace an existing Format (drop into the MDE) or add the format to an
empty book. The metadata is not reread from the book.