I've had my Global Link account since the games release. Today when I signed in to the Pokemon Global Link website after using my Japanese 3DS with US region emulation on a legit US cartridge for Ranked online play via the latest Luma 3DS, linked to a US Global Link account, I received this message on the website:
It appears there is a low level check of the consoles region that it associates actively with your save file when using consoles of different regions. I believe this was also the case for the previous 3DS Pokemon games but I don't think it completely affected Global Link in this way as long as when you first created the Game Sync ID it was on a US 3DS (Otherwise it would create a Japanese Game Sync ID even though the game would be in English). I would really like to know if there is anyway to bypass this region check.
It appears there is a low level check of the consoles region that it associates actively with your save file when using consoles of different regions. I believe this was also the case for the previous 3DS Pokemon games but I don't think it completely affected Global Link in this way as long as when you first created the Game Sync ID it was on a US 3DS (Otherwise it would create a Japanese Game Sync ID even though the game would be in English). I would really like to know if there is anyway to bypass this region check.