There has now been an official English translation of Nintendo's notification, which advises that the fix in question will be an application to download from the eShop; this will then restore corrupted save data. There's also an English version of the map, showing the blue areas to be avoided when saving your game — thanks 123akis.
Earlier this week we reported on a game breaking bug in Pokémon X & Y that was affecting some gamers in Europe and Japan; it was discovered that — occasionally — saving in Lumiose City can cause irreversible corruption of save data, forcing the unfortunate players to start all over again. Nintendo has now acknowledged the issue and advised that it's working on a fix.
Posted on the company's Japanese website, the message — allowing for some quirks in translation — suggests that work on a fix is under way for those that have experienced the problem, with a "few days" apparently mentioned though, to be safe, let's just treat this as a case of "as soon as possible". The post acknowledges Lumiose City — or Miare City in Japan — as the source of the issue, with advice to save in buildings such as the Pokémon Centre. The map below reportedly shows areas that prompt the bug.
As mentioned above, the fix will apparently deal with corrupted files, so if you're happy to wait you may not have to restart the game. We'll keep you posted on further updates.