Spent hours last night painfully transferring nearly 40 apps from a standard DSi to the 3ds, some failed and restarted, and all the others went fine...
I don’t think it is actually transferring anything from one device to the other, as one of mine failed and the other one carried on.
It looks like the source device talks to the Nintendo server which then talks to the target device. the app/game is then pushed to the target device from Nintendo’s server (that’s why no saves go with it, and why some can’t be transferred) the source device already has the app deactivated and deleted from it at that point it just shows a screen looking like its talking to the target device.
Once the target device has received the app/game both devices are set to continue.
I had one fail and the source device stayed like it was transferring. I turned of the source and restarted the target and was asked if I wanted to continue, which it did, with the source device off. When I put the source back on, disconnected from the network the game was gone and you couldnt copy it back from the SD card as the cert was removed from the source device.