A method of maintaining patient registration in surgical navigation includes: obtaining a patient position in a tracking system frame of reference, based on a fiducial marker array affixed in a first position relative to the patient； receiving an initial surface scan depicting the patient and the fiducial array； responsive to receiving an intraoperative image depicting the patient: obtaining a position, in the tracking system frame of reference, of the fiducial array affixed in a second position relative to the patient； receiving a secondary surface scan depicting the patient and the fiducial array； detecting a deviation in a position of the fiducial marker array relative to the patient between the initial and secondary surface scans； and applying the deviation to the position of the patient to generate an updated position of the patient in the tracking system frame of reference, based on the fiducial array affixed in the second position.
