Here is the full list of all 16 Ys VI: The Ark of Napishtim achievements. It takes around 15-20 hours to unlock all of the achievements on Windows.
Acquire every Tabulas.
Destroy the Ark’s Central Shaft.
Defeat Ernst.
Acquire all equipment.
Win a boss fight without taking a single hit.
Defeat Orjugan.
Defeat Ud-Meiyu.
Defeat Zonplas.
Win the duel with Geis.
Defeat the Wandering Calamity.
Defeat Majuunun.
Win a boss fight with 1 HP remaining.
Complete the game on Nightmare difficulty.
Complete the game in Catastrophe Mode.
Complete Boss Rush mode on any difficulty.
Obtain every other achievement.