You're going to have to get them hard modded assuming you have the backups. Personally, I think you should have only performed on 1 3DS at a time, and put files in each their own seperate folders.
My suggestion if you are able to try again.
If you either restore, or buy a new system, set any other 3DS aside, don't touch them. When you start the instructions, make a new folder on your desktop, inside each folder, make a new folder for each part of the tutorial.
So PART1 will hold all the downloads and files you use for that page ONLY. When you go to PART2, go back, make a new folder outside, and do the same, even if you have to redownload what you already have. Even put your backups in a folder inside the part folder where you make backups. I think PART4 is one of them. It's the safest way to do this. I actually A9LH'd my European N3DS yesterday and I'm very happy with it. You just need to be VERY careful while doing this mod, and don't get impatient. It took me 5 or 6 hours to do mine on a freshly formatted 9.2E system with a blank SD card. Once I get a copy of Cubic Ninja for my main 10.7 system, I'm comfortable enough to try again, but this time, retaining all of my stuff.
EDIT: Like this. Only folders and ZIPs are showing. My otp.bin for my N3DS EUR is in the root of PART4.
EDIT2: ALSO, when you're done, I also recommend you do something like this. Make a MEGA Account exclusively for 3DS backups with a brand new garbage email and password you've never used, put your NAND's, SDCard Files and OTP.bin in a directory on there, write down credentials on a small piece of paper, fold it and put it into the back of the back plate. That way, if you brick, you can just go into the back plate and everything's there. If you resell the system impulsively, obviously you're not using a personal EMail and Pass, so really, all you're losing are NANDs and console specific files you'll never use again anyway.
