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I had my warboss beheaded in close combat by Captain Sicarius in a game last night (How embarrassing ).

Do his full number of wounds count for determing who won combat?

Reading the relevant sections in the rulebook left me unsure. I gave my opponent the benefit of the doubt and counted the full three wounds in his favor, but I'm still not sure...

Yes, read page 39 of the rulebook.

BRB, Pg 39 wrote:

-only wounds suffered by enemy models (including all of the wounds lost to ID).....

So, you were correct If he lost 3 wounds then he lost 3 wounds.