Because of past PGL ban waves (and a potential future one), many are wondering if they can edit save files safely. The safest option is to simply not hack or to not use game sync, although some minor edits may be safe. The problem is that it is unclear on what the bans were based, and the Pokémon company hasn't exactly volunteered this information.
Here are the known causes of PGL bans:
Getting 999 of every item (it's possible the bans are from a sub-set of items)
Making illegal changes to Pokémon between game syncs
Illegal Pokédex entries
Items in the incorrect Bag Pocket
Changing anything in the save that is static (like OT, Gender, Language, etc.)
Getting all clothing (there's been mixed reports about this)
We have not received any reports of banning due to receiving hacked Pokémon in trades. Making other edits might be safe, but only as long as the result could have been accomplished without hacks given more effort.
By hacking your save file, you accept full responsibility of any consequences such as being banned. If you are banned, however, we would appreciate your input so we can learn more.
Thanks to everyone who posted in our previous threads about the bans for sharing their experiences, zenamez of GBAtemp for compiling the causes reported on GBAtemp, and to theSLAYER and Serebii for checking this information.
Image Source (Thanks to @\ from our IRC for suggesting this)
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.