While I never did go online to do battles with the cartridge in a different Region 3DS,
I did accidentally use the same save (on a different Region 3DS, pre-GameSync) to collect a wonder card for screenshots,
(which I remember the incident very clearly), so that is how they caught me.
I probably went online without checking my Luma's Region setting.
(it was set to a different region settings, argh)
According to the Japanese Pokémon Global Link website as reported by Serebii.net,
7,651 more players have been hit with the 090-0212 ban wave, after being detected of having a modified game save.
This ban bars users from accessing Online Play services (Game Sync, Battle Competitions, Rating Battles, Global Missions).
Once again, The Pokémon Company has announced that they will continue their pursuit against people with edited save data.[1,2]
If you are affected by the ban, please let us know what kinds of edits you made,
so we can get a better idea what The Pokémon Company is looking for.
While we already some strong suspicions regarding the causes previously,
we urgently recommend not going online if you modified your save, until we have more information on how these bans were triggered.
@Dio_Vento has recently released his ROM hacks of Pokémon Sun and Pokémon Moon. Based on his previous work, Pokémon Rutile Ruby and Pokémon Star Sapphire, these hacks aim to provide a legitimate challenge to players seeking something more from the latest Pokémon games.
Here's the trailer:
Features include (but are not limited to):
Harsher level curve
New trainer & gym teams
NPC's using Mega Evolution
Improved item availability
Trade-based evolutions can be done in-game
Downloads, as well as more information, can be found in the project thread.