When the reference point is temporarily covered by another object, position the tracker box manually.
When you manually position the tracker box, the new position is recorded in the Track X and Track Y channels of the Channel Editor. These values have precedence over the Shift X and Shift Y values.
To manually position the tracker box:
Since the X and Y shifts are recorded as keyframes in channels, the Stabilizer calculates the translation values for the frames in which the reference point was covered. The final result will be a smooth motion.