ray, what type of foundation are you using the bees died in?
i use waxed plastic, when i have a dead out, i tap the frame against something solid a number of times to get the majority out, and will lose a little comb if i get carried away(bees will fix that)......and yes i have used a needle to pull them out if i have too.....
because i have too many boxes i keep and store to remember which box has the dead bees in it. i don't like to store comb with dead bees in them for an extended period of time. get's moldy.
like barry said though, a strong colony will remove dead bees, i like to get as many as i can out before storing or returning it to 'service'.