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@SamTzu - I'm confused. I assume you're referring to the 'custom covers' created by the Generate cover option in Metadata edit?
Nothing is saved from the metadata edit dialogue until you exit the dialogue via OK, Next or Previous, that's when the Book details panel on the main screen will change
AFAIK the 'I' button in metadata edit dialogue 'extracts' the cover and metadata from the selected format file. The tooltip for the 'I' has - "Set the metadata for the book, from the selected format', which seems to be the opposite of what you're suggesting it does.
The book format files (EPUB, MOBI, AZW etc) in the library do not get updated when you change the cover or metadata. There are several ways to 'inject' the metadata and cover into the book format files - in the output of send to device or save to disk, Polish (EPUB and AZW3 only), Embed Metadata (most formats), the Modify optional plugin (EPUB only), and conversion.
You may need to use Preferences->Toolbars to get the Polish and/or Embed icons into your toolbar, you need to install the Modify plugin, via Preferences-Plugins->Get new plugins if you don't already have it.
BR
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