Copying over the existing directory will keep your settings. You'd either have to delete it completely, or only delete reader.settings.lua and the settings subdirectory. That being said, take a look in settings → highlight action to see what it's set to first.
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the file browser is also a bit wonky, for most folders it says there are items, but when I navigate in them, there's nothing there.
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The system doesn't dive into subdirectories for performance reasons, so it's arguably better not to list any number at all. The number of items is all that can be known more or less for free, not whether they can be opened.