I have a few question regarding Toughness and ranged attacks.
1. There are some cards where a unit takes a hit in order to attack as one rank higher unit. Can toughness negate this effect while unit still gets the bonus?
2. Damage when unit gets black (retreat) flags rolled against it and can not retreat. Can toughness prevent this damage?
3. Do cover (in house) bonus and toughness stack?
4. Ranged attacks and directional retreat - if unit is hit with a ranged attack (black flag) that causes unit to retreat - must the unit retreat away from a direction from which attack came since this is not melee attack?
1. No. It is clarified in the rules that commanders cannot take hits to trigger tactics on order cards. And I believe that the designer also clarified that toughness cannot be used to trigger tactics for free, because, technically, your unit didn't take the hit. That might be a clarification that the designer needs to add to the next FAQ/Errata, if it's not already there. I don't remember.
2. Toughness prevents the first hit and inability to retreat is counted as hits, so, yes, if it is the first hit, toughness will negate it.
4. Clarified recently by the designer. Will be in the next FAQ/Errata document, hopefully. Ranged attacks trigger "normal" retreats away from the opponents side of the board. Only melee attacks trigger directional retreats.
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