Alright, so I made the terrible mistake of falling asleep during the transfer from my 3DS XL to my New 3DS XL and the old one died while I was asleep. I redid the transfer after waking up. Ever since then, everything with my New 3DS has been going wrong. For a whole week since the night the New 3DS came out, I've been struggling just to keep my games in one place.
Some games would only show the icon on the home screen but tell me I need to redownload. Some games would not allow me to redownload due to error code 005-2999. Some games would randomly stop working on the home screen when they would work. I would always back up the SD first and then try injecting the save file from the SD card "title" folder. Every time I tried this, a different game would corrupted and unavailable for download. After several failed attempts, I decided to accept my mistake, let go of my save files and just decided to reformat the SD Card and redownload the games. I thought this would surely just let me play them normally since I stopped tinkering with the save files so much...
Except it didn't. I redownloaded Animal Crossing on the wiped SD Card and it gave me several errors mid game that would send me to the home menu. Loading it up would just give me an error. I DID discover the eshop's Software Repair Tool and it seems to have fixed the issue, but I cannot trust it at all. After doing the repair, I rechecked it a while later and it said that the software needed to be repaired again. I ignored and rechecked a while later and it said that it was fine. It also said Shovel Knight, which I hadn't even loaded up for the first time after redownloading, needed repairs so I did. Afterwards, I set several of my games to download later on the eshop and tried to play Smash to kill time. Guess what? I loaded Smash, which was a physical copy, and all it gave me was a black screen. Deleting the update and redownloading APPEARS to have worked but I just cannot trust it after everything that's happened. I'm afraid that turning off the system mid transfer just ruined SOMETHING on the system. I don't know what step it even shut down on, I just woke up to an error. Should I send my system in for repairs? Would the warranty even cover this mistake I made? I just want to enjoy my shiny, new system without any weird problems, but I also do not want to invest time in a new save just to encounter another problem that will make me lose it... 