A method of tracking a position of a catheter within a patient includes securing a navigational reference at a reference location within the patient, defining the reference location as the origin of a coordinate system, determining a location of an electrode moving within the patient relative to that coordinate system, monitoring for a dislodgement of the navigational reference from the initial reference location, for example by measuring the navigational reference relative to a far field reference outside the patient's body, and generating a signal indicating that the navigational reference has dislodged from the reference location. Upon dislodgement, a user may be provided with guidance to help reposition and secure the navigational reference to the initial reference location, or the navigational reference may be automatically repositioned and secured to the initial reference location. Alternatively, a reference adjustment may be calculated to compensate for the changed reference point/origin.