It's not burn in. These artifacts happen if the LCD is turned off while drawing/showing something other than a completely black picture. This does not cause any hardware damage and you can ignore it.
I'd be interested trying out 3D videos on the 3DS even though I could never really get that 3D experience from 3DS games.
Do CIA files of 3D movies exist? Not where, rather do they truly?
The same happened to me with luma config screen. Just remove your battery from your system for about 20 second. Insert your battery back and start your system. No more Ghost screen.