Hacking What is the safest way to update .CIA games

[cearp]

one of the things I've noticed is that eshop titles don't update if they're a different region from the 3ds eshop where it gets the information/nag that there's an update. chances are that if the install goes through, the game will still nag you that there's an update. you can find a list of updates in fbi or find the region of the game. I think this is even true (not updating through the eshop) if a game has been made region free, at least I've encountered it.

yep that will be true, as 3ds/eshop is region locked.
so if you have the Japanese version of animal crossing on a USA 3ds, you will still get an update nag, but no possible way to update via that nag.
If the game is pokemon sun, same game and title id for all regions, then you'll get the update nag and will be able to update.