urgh. At the very least, you should know what you're doing and what CFW you're using.
Looking at your second picture from earlier, there's no Luma folder, and there's a Steelhax folder, so I can only assume you're using an old CFW entry way using Steelhax or something.
Now, to go back to your main issue. If you dumped the save from the VC game, and edited said save with PKHeX, no reason for the save to not work.
You're using a different save manager (that I've never heard of), so the best advice I can give you is to remove main from that folder, only then try to restore it. (I know the main is your other save, but who knows if the entire folder is being squeezed back into your game. And if that's the case, main should not be there)
If it doesn't work, then I can't help you. What you need to do is to update your CFW, and please use an updated text guide as opposed to a video. It's imperative that you at least try to understand what you're doing. (Also, any 3DS can be hacked, you just need the requisite accessories).
Finally, use JKSM or Checkpoint. We have tutorials on our site regarding backing up and restoring saves using either of those methods.