Since Nintendo seems to be failing in the tech support area I wanted to post what has been working for me... after 6 hours of trouble shooting! My delema was I opted for the pc transfer as Nintendo suggested for people who have purchased large games from the eshop. Everything backed up on my old 3ds perfectly, plug the sd card into the computer and start copying to the desktop and files 0000000.app will not transfer. These are the actual game files. At first not knowing what to do I skipped over them transferred to my micro sd and plug it into the system. i am thrilled when my home screen looks just like the old one and the game files are there.... then I try to open one and it instructs me I need to redownload it from the eshop. Go into the eshop, activity, find the game, scroll to the bottom and click repair. The eshop analyzes my file, says it needs to be repaired and takes me through the download menu. I plug my new 3ds into the charger and go about my business. 2 hours later and it hasnt even begun to download! New 3ds is frozen, have to force a restart, now I cant get into the eshop. I took the micro sd card out and recopied what was on my desktop, plugged it into the new 3ds and we are back to the beginning.
The solution i have come up with is to go through the data management menu in the 3ds setting, delete all eshop downloads, go into the eshop and redownload my games. I would only do a few at a time if you have a lot because we need to take the micro sd card back out and look for the .sav file that is on our desktop. If you only do a few titles at a time its easier to figure out which game is which. Looking at the back up saved on your desktop Nintendo 3DS>jumbled numbers and letters>jumbled numbers and letters>title once in the title folder you will most likely see 4 folders
0004000e - updates
00004008c - DLC
000040000 - games and save files
000040002 - Demos
most game files have 2 folders in them content, which I think is the actual game, and data where the .sav file is located
hope this helps