As others have said, Handbrake doesn't passthru cover art or thumbnail images. If you wished to add cover art to a Handbrake encoded video file, use MetaX. It's not free, but will add cover art and text that Plex, iTunes etc. Will all recognize. Source: almost 2 years ago
MetaX tags videos, adding cover art, genres etc. And allows you to specify a chapter interval and create chapters to fit the length of each file. It will tag a single file or a batch of files in a single process. MetaX is not free. Source: over 2 years ago
MetaX works great on MKVs on Windows. You can find it here: http://danhinsley.com/metax/metax.html. Source: almost 3 years ago
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