Workaround
This is not perfect, but...
Armor encumbrance reduces your AP. Furthermore, ranged weapons are not affected by encumbrance, as they do not give fatigue. So... assuming you're just modding the Chu-ko-Nu units... you can give them a low AP by leaving the AP at 12 but awarding them a special armor with a very high encumbrance. Real AP = min((Base AP - Encumbrance), 2), I think. But maybe the minimum is 1.
I don't ever remember having problems with AP when modding. It sounds to me like you are setting AP before you do some #clear command, so the AP is reset to 12 and subsequently reduced to 11 by armor encumbrance. Are you sure the unit definition commands are in the right order?
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