With last night's update, there's now a tool that let's you move saves from physical retail games to their downloadable versions. So if you got Mario Kart 7 at retail and bought the digital version of Mario Kart 7, you can move your physical save of MK7 to your digital copy of MK7.
HOWEVER, once you digitize your physical save, it's stuck as a digital save forever. You can't move your digital save back to your retail copy. FAIL.
3DS eShop now has a "Repair Software" option in that if your game/app is cutting up on 3DS after you just downloaded it, you can go to the respective eShop page for the game/app, go to "More Details", and tap on that "Repair Software" button on the bottom of the page.
So now you don't have to delete and redownload the game/app unless the "Repair Software" option fails to fix your problem game/app.
Yet again I misinterpreted your meaning (though it's none of your fault).
At first I thought you said there is a tool that lets you move your GAME from a Physical Copy to a Digital one, so I could install my Mario 3D Land on my 3DS and render my physical cart useless by having it corrupted/erased in yet another one-way operation. At first I thought that was pretty fucking sweet since not all physical games are available in digital form. Well, at least I had the "one-way operation" part right... fuckin' Nintendo. :dry:
Anyway, I don't get that Repair Software part. So is this in case your kill the power during a download/installation and your rom gets corrupted and you need it replaced/repaired? I don't think digital copies get fucked up any other way.