An affirmative statement asserts an event without negating or questioning it.
«جَاءَ الْقَوْمُ إِلَّا زَيْدًا» = The group arrived except Zayd.
Complete: the group is named.
Affirmative: no negation is present.
Hence the exception is accusative: Zaydan, not nominative Zaydun by the ordinary substitution option.