An ion implanter includes a source of a stationary, planar ion beam, a set of beamline components that steer the ion beam along a normal beam path as determined by first operating parameter values, an end station that mechanically scans the wafer across the normal beam path, and control circuitry that responds to a glitch in the ion beam during implantation pass to (1) immediately alter an operating parameter of at least one of the beamline components to a second value to direct the ion beam away from the normal beam path and thereby cease implantation at an implantation transition location on the wafer, (2) subsequently move the wafer to an implantation-resuming position in which the implantation transition location on the wafer lies directly on the normal path of the ion beam, and (3) return the operating parameter to its first value to direct the ion beam along the normal beam path and resume ion implantation at the implantation transition location on the wafer. The operating parameter may be an output voltage of an extraction power supply, or other voltages and/or currents of beamline components that affect the path of the ion beam.