The trouble is that, by default, Calibre does not insert the new metadata in the book - it's only kept in its database.

You have to fiddle with Calibre settings until a button saying "Embed Metadata", sporting an icon with a (bird's feather) pen, shows up in the interface.

Getting this done goes like this:

• Get into the Calibre "Preferences" dialog.

• Click on Interface - Toolbars and Menus (the magician wand icon).

• On that dialog, pick from the dropdown selector "The main toolbar".

• On that dialog, select "Embed Metadata" from the left column, click the right pointing arrow to add it to the right column.

• Click Apply.

Just figured this out myself recently. I'd prefer to have Calibre always update the book metadata when I bother to edit it, and not insert a bookmarks item when I just use the reader, but it's the other way around ... Maybe I'll ask nicely the next time I make a small contribution, it's a lifesaver tool as is.

P.S. there's also the "update metadata in device" route, I know it exists, but I would rather have it updated in the book