Since version 1.9.0.3 beta 11 you can only scrape missing media (artworks) by checking Missing media only (formerly Without Artwork only) in the Scrape Options tab. Only missing media (artworks), checked in the Images options tab will be recovered.
In the scrape engines, only these missing media (artworks) will be presented and selectable.
See:
Scrape only missing Artworks (media)
It is possible to scrape only certain media without touching the existing Mixes
Video Tutorial
Watch video
These media are:
To do this you must:
'Get the video',
'Get the Manual',
'Get Map',
'Get Fanart',
'Get the Titleshot'
'Recover Boxback'
'Theme Hyperspin'
'Recover Extra1'
'Round Wheel (HFSDB / Screenscraper)'
'Get Screenshot'
'Get the Boxart'
'Get the Wheel'
'Retrieve Cartridge'
'Overlays (choose format 4/3, 16/9, Custom…)
When you are done with the manipulations of the Database, remember to save its content in the gamelist.xml by clicking on the button 'Create gamelist.xml'