Are there any permanent events or missable items in the game?
There are no permanent events or missable features in Ni no Kuni 2: Revenant Kingdom so feel free to clear the main story, side quests, errands, and other objectives at your own pace. All side quests (including rewards such as equipment, higgledies, and recruitable citizens) can be accessed even upon clearing the game as long as they have been unlocked through specific conditions.
Useful Things to Remember
Do not sell stinky or smelly shoes until you have completed Side Quest 117: The Sweet Stink of Success.
As you progress through the main story, you may acquire shoes with the “stinky” modifier in their names from monsters defeated in battle. If you do manage to get one, do not sell it. This piece of equipment is actually one of the items you will need to deliver to Morgan to clear Side Quest 117: The Sweet Stink of Success.
Stinky shoes are quite rare and seem to serve no special purpose apart from being a target item in the quest mentioned above. If you accidentally sold them off, you will need to farm the enemies found in the Dreamer’s Door at the Grotty Grotto. Alternatively, stinky shoes can also be purchased from the merchant’s random stock at the grotto’s first level or may sometimes be acquired from chests in the area.
Note that some players have reported to have farmed the Grotty Grotto for several hours before obtaining a single piece of stinky shoes so do not sell them to spare yourself from the tedious chore.