If there are several flights taken under different weather and lighting conditions, I can suggest to split them into difference calibration groups in Tools Menu -> Camera Calibration dialog. Each group should contain the corresponding images of the panel, as each group will be calibrated separately.
And if all the flights are in the same calibration group, then the answer to the question depends on the presence of the calibration images both before and after all the flight images. If this condition is fulfilled, then the interpolated data will be used. And if the calibration panel images are taken only before or after all the flights, then no interpolation will be applied and single set of the calibration images will be used.