woodruff keys would explain it, the bolt only holds the hb and timing gear in place but these are a bastard to get out even without the bolt.
in an engine in bad shape its possible to shear them off, although i havent seen it happen.
what it MAY be, but this is purely my idea and may be completley wrong...
someones taken your HB off and lost a woodruff key in the process (your crank has 2, one for the timing belt gear which sticks out a bit into the HB, and one mainly for the HB). they might have thought it would be fine on the one sticking out of the timing belt gear.
its either that or your HB woodruff key has sheared off completley which would explain your car still running ok from the woodruff key still attached on the timing belt gear (otherwise you would have done serious damage to valves, pistons from cam timing being off).