I beleive they should be done cold, due to the expansions of themetals and so forth, i am not too sure on the particulars but i have experienced it before if you put a bolt into something warm or hot when it cools down it basicly gets locked there forever.
technicly you should replace your head bolts each time they are undone but i know no one ever does it including me. it is to do with the stretching of the bolt when it is torqued down.
what you should do is take the bolt right out when you go to retorque them put a thin smear of oil on the thread, inder the head of the bolt and under the washer of the bolt if it has one, this is to reduce friction and give a true torque reading.