#1.....just had a quick test on my n3DS and just got "no card detected after connecting to the server"...with NDS or 3DS games, so I'm not sure if it will work, probably down to the fact the 3DS detects when the cart has been removed or whatever
#2, nope pokemon games are card2 which means it uses different save methods, i doubt dsavemanager would support reading cart2 saves
well a clean legit rip of pokemon OR/AS installed in gateway mode, then used in combination with classic mode and the save data transfer tool would allow you to carry a 6.x save over to a digital copy....then if you wanted your free to use SDF on the digital save
or he could just play pokemon in classic mode with the retail cart so he can keep his save until their is a solution.
I totally forgot that Save Data Transfer tool existed. I might have to do some playing around and see what I can do .