The commander can determine the event with input from the health care professional. If the doc says bike and swim and the commander says bike, get ready to pedal!
Extracted from TC 3-22.20:
Soldiers with temporary physical profiles must take a regular three event APFT after the profile has expired. Soldiers with temporary profiles of long duration (more than three months) may take an alternate aerobic event as determined by the commander with input from health-care personnel. Once the profile has been lifted, the Soldier must be given twice the length of the profile (not to exceed 90 days) to train for the regular three event APFT. If a regularly scheduled APFT occurs during the profile period, the Soldier should be given a mandatory make-up date for the APFT.