That error is probably because you don't have the aeskeys bin on your sd card.
Restoring the nand with hourglass9 should fix your issues unless your emunand itself is already corrupt.
You will still need the aeskeys bin on the root of your sd card for decrypt9 to work properly.
Thanks for all the help, but everything is fine now.
I removed my pokemon Y cartridge and put it again then the 3ds reconized the cartridge again and the game have a obligatory system updated to nand 6.1, then after that I could use system update to the latest firmware.
After that I could easily do the last two steps in the Plailect guide .
More easy to resolve than anything in the end, lol.
Just for curiosity, every icons from my Emunand where deleted after the updates, but who cares.
In the end, my pokemons saved my day !