So I have had a nightmare scenario with my system transfer. If anybody has any advice, I'd really appreciate it.
I have a 32gig SD card in my original 3DS, and I just purchased a 32gig microSD card for my New 3DS. I plugged it in and started a full transfer. It looked like it was going to be a multi-hour affair (as expected), so I let it run for a while. I came back to see that a local wireless error occurred mid-transfer, and I was told to try the transfer again.
I did so, and I received the same error within just a few minutes this time. Nervously, I tried one more time...
...And this time it worked! But it only took a few minutes? Seeing as how I expected it to take hours, I was becoming suspicious. My fear increased when my New 3DS asked to transfer my DSi games from the SD to the system, but claimed no games could be found when I confirmed the transfer. It then said, if I wanted to continue without transferring (which I couldn't do), then it would delete my DSi games (which it just claimed were nonexistent).
On my home screen, I saw all of my games and their icons, but none of them would play, and the theme shop did not acknowledge any of my previous purchases. I went to the eShop, where I was informed I could repair my downloaded games. I started with Alpha Sapphire, but it immediately hung up and wouldn't download anything for an hour, at which point I powered down the New 3DS.
Now my home screen shows none of my games, and I can't connect to the eShop (Error Code 007-0200). I can't do anything.
I called customer service (twice), and I've been able to confirm my purchases/licenses have transferred successfully. However, they suggested my (newly purchased) microSD may be bad. I can either format the card and re-download my games, or send in my New 3DS for Nintendo's repair guys to see what could be wrong.
However, I'd rather not lose all of my save files, which I think would happen with both options. Any suggestions? Is it possible for me to copy save files to my desktop, format the microSD, redownload the games, then copy over my save files? If so, where can I find the save files?
Also, strangely enough, my original SD card seems to have a ton of data still on it, even though my 3DS said it was going to format it after the transfer. What's up with that? Is it possible some of it could be save data that could be salvaged?
EDIT: Crisis averted. Contrary to what I was told through customer service, only system memory was reformatted on the old system, not the SD card. And all of the data on the old SD card was compatible with the new microSD card and the New 3DS. I just copied it and everything seems to work now.
I should have transferred the SD card data via PC from the start. Much easier and quicker than dealing with a multi-hour wireless transfer that is prone to disconnects...