Hello! I've got a very strange issue going on here that Google has not been able to help me with.
I bought a red New 3DS the other day, and performed the system transfer from my old Animal Crossing Special Edition 3DS this afternoon. I chose the "PC Transfer" option, and everything went smoothly at first.
However, when the new 3DS restarted and brought me back to the Transfer screen, the internet unfortunately had a hiccup and timed out, and I was brought back to the Home screen. The first thing I noticed was that the Home screen had been reverted back to the default theme, instead of the current one I was using. My folders were still there, albeit devoid of all my downloaded software save a few games; the Pokémon ORAS demo, which I hadn't placed into a folder, was also missing. Thinking a restart and removing/reinserting the microSD card would fix things, I hit the power button, but as I did, a message suddenly popped up about adding new software to the Home screen. When I returned to the Home screen, the message was gone.
A restart/reinsert seemed to fix the problem. My theme was back, but I hadn't checked the folders yet. I had a StreetPass notification left over from my old system, so I tapped the Notifications icon, checked the message, and then went back to the Home screen...which had reverted to the default theme once again. This time, a restart/reinsert didn't fix things, so I put the microSD into my laptop to check it out.
The card wasn't corrupted and was accessible, and the data hadn't been wiped. Everything still seemed to be intact, so I transferred the contents to my desktop just in case (yes, I know I should have done that before, that was a stupid mistake on my part). I went to the System Settings to see if the system recognized anything, and this is what I'm seeing now:
You can't really tell from the picture, but the icons are greyed out in addition to having the X's next to them; I've never seen this before, but I can only assume it means the games are corrupted somehow, even though it says they're still taking up blocks on my system. What should I do in this situation? Should I wipe and reformat the microSD and try again?