Well, I was kinda expecting that to fail, because I don't know much about programming and coding, but I think that the backup save file from Decrypt9 and the save you downloaded from the internet are not the same kind or differ in some part of the code. Unless you can find a backup made with Decrypt9, I doubt you'll be able to inject a save file that someone uploaded, even between emulators and flashcarts you had that problem.
I remember once I copied my Digimon Story Lost Evolution save file from my Acekard2i to my computer and NO$GBA wouldn't read it, but DeSmuME did. I think this is a similar situation, so if you want a 100% completion save of any game, to then inject it on your 3ds, you're gonna have to ask someone to upload it. It should be possible, after all you're already transferring the save form one console to the other, so if I were to give you my Minish Cap save, you should be able to inject it with no problem.
Anyways, I'm sorry I can't help you more, but as I said I lack the sufficient knowledge to find a solution. I bumped into the 8kb solution by simple chance because I was curious to know if my theory of the need for a pre-existent save file on Console B would solve it. It turned out to be half of the solution, but I wouldn't have find the other part of it if the HB Launcher hadn't crashed. Keep making tests, with a bit of luck you might find find the solution.