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battle, the equipment destroyed bonus missions or oaths will NOT count towards your overall bonus after you complete the mission, even if you take no damage or have less than 5 parts of your armor broken (which can be bypassed by transforming).
There's those types of bonuses that do not count unless the game fully registers the kill, which will take around 16 to 20 seconds to do so after killing said boss.
It's one of those "things" that ruins the potential of speed running a dungeon.
This.
The system message will also warn you if you complete the dungeon too fast. (less)