Most recent 'not working due to new anti-piracy' seems to be the recent Japanese release of Pokemon Super Mystery Dungeon.
I'm intrigued to know whether the recent US release of ACHHD also has the new AP, but I've not found a rom of the retail release yet.
Latest was probably the wrong word, I just meant we can assume all of the upcoming first and second party titles will have the new AP. Also the NA version of HHD seems to have it too.
Yes, it seems that AC:HHD is the first non-japanese title to carry the new AP that renders it inoperable on the Sky3ds. Sky-team added it to the template, but no ones been able to get it to work.
...so, the titles affected still stands at Fire Emblem: iF (JPN), Animal Crossing: Happy Home Designer (JPN, USA, EUR), and Pokemon Super Mystery Dungeon (JPN).