Having boarded a New York City-bound flight Sunday in Arizona, the rocker's private jet first touched down in Nashville.
Michaels was "complaining of a headache, lower back pain and some cramping in his legs," sources at the airport tell PEOPLE.
After a brief stop, Michaels, 47, re-boarded the aircraft and is currently en route to New York.
Earlier in the week, the singer's spokesperson had said their team was "cautiously optimistic" about Michaels' attendance at the finale, just days after suffering a "warning stroke" and a month after experiencing a subarachnoid hemorrhage.
Reporting by ANNE MARIE CRUZ