Thank you, it worked flawlessly and I had no issues so far.
Dumping it again is out of question, especially because as I stated before, I factory resetted my 3ds and backed up all my games on JKSV. Most of backups transferred just fine, these two Pokémon games were the only exceptions. Even Pokémon X worked fine.
I'll double check these backups next time, and already made the changes on FileZilla so hopefully these issues will never happen again. Thanks for the help, everyone.