To clarify; The camera card has the Autopilot UPDATE FILE, not the actual Autopilot. The actual Autopilot is part of the drone.
Since you want to keep the existing firmware on the controller, the sequence should be:
1.) Do the camera card section of the update.
2.) Rebind the camera and drone to the controller if needed.
3.) Verify the new firmware versions are correct.
4.) Do the calibrations.
5.) When all calibrations are complete, ensure the camera is removed.
6.) Do a few test flights with NO CAMERA.