Back in mid-May Citizens of Earth was taken off the 3DS eShop as a result of it being used for a homebrew exploit. As per Nintendo's current policy, exploits released online are rapidly (often within 24 hours) counteracted by the removal of any apps or games that are being utilised. The developers in question are, ultimately, innocent victims that see their games removed from the store.
Though it's taken around 2.5 months, publisher Atlus (the game was developed by Eden Industries) has got the game back onto the eShop. It seems any changes have been substantial in order to close any exploits, too, as there's also a sizeable update to the game.
In any case this is good news for both Atlus and Eden Industries, as sales can resume of the portable version.