Basically it patches the QR codes so you can't use PkHex unless you have a flashcart.
SourceSo, looks like there's some new updates available:
- Pokémon X and Y: version 1.4. Usual "bug fixes" meant to improve the game experience for all players. Update is required to use the online features of the games. It requires 246 blocks.
- Pokémon Omega Ruby / Alpha Sapphire: version 1.3. Usual "bug fixes" meant to improve the game experience for all players. Update is required to use the online features of the games. It requires 271 blocks.