I finally found the problem that was causing the favoured weapon skill checkbox to not save properly. The good news is that this means that the favoured weapon skill state is now saved, and it can be used to do macros like this (NPC vs. Adversary, first weapon), one of a series of macros I'm experimenting with that makes setting up characters and having them duke it out with each other a lot easier.

/emas @{selected|token_name} attacks @{target|token_name} (TN #pc_vs_npc_defense ) with a @{selected|repeating_npc-weapon-skills_0_npc_weapon_skill_name} (Damage @{selected|repeating_npc-weapon-skills_0_npc_weapon_damage}, Edge @{selected|repeating_npc-weapon-skills_0_npc_weapon_edge}, Injury @{selected|repeating_npc-weapon-skills_0_npc_weapon_injury}, @{selected|repeating_npc-weapon-skills_0_npc_weapon_called_shot}, Damage Bonus @{selected|attribute_level}).

/r 1t[feat] + @{selected|repeating_npc-weapon-skills_0_npc_weapon_rating}t[@{selected|bar3}] + [[@{selected|repeating_npc-weapon-skills_0_npc_weapon_skill_favoured} * @{selected|attribute_level}]] + ?{Modifier|0} > #npc_vs_pc_defense

This uses the Favoured Weapon Skill State to calculate whether the NPC gets to apply his Attribute Level to his roll (because the Favoured Weapon Skill State is 0 or 1, it's just multiplied with the Attribute Level).

The bad news is that because the new 'true' value of '1' is different than the old one (which was 'on'), all characters will lose their Favoured Weapon Skill States. Sorry about that. I try to not break things going forward unless there is no other way, and in this case it was a matter of me not understanding how Roll20 saves default data (I still don't understand why anyone would want 'on' as the default value over 1, which is much more useful in dealing with macros, but whatever).