I haven't tested it, but I'd say it's a pretty safe guess that internal cake temperatures (below boiling) are not sufficient to cook away any caffeine.
I haven't worked much with mole but a dry rub containing coffee might lose some caffeine if a sufficient temperature is reached.
What it boils down to is this, is it hot enough to turn the beans a darker color? If you reach that temperature some caffeine will be lost. How much? I would have to guess that it's pretty negligible. Definitely not enough to remove all the caffeine from decaf nor enough to turn caf into decaf either. Not to mention the propensity in this equation for burnt coffee. I'd leave coffee roasting to the professionals.
I really don't think there's much that you can do, as a chef, to control caffeine content in your food other than to choose brands of coffee that have less caffeine to begin with.