Hello ArnauCM,
If you would like to have sub-sets of images be calibrated using different radiometric panel images, you need to split the calibration groups (via Tools Menu -> Camera Calibration dialog) so that each group contains the set of calibration images.
The easiest way is to add the images corresponding to each sub-set to separate chunks and then merge chunks before performing any processing operations - merged chunk will have the Calibration Groups split according to the original chunks.
Note, however, that inside each camera calibration group the interior orientation parameters would be estimated individually, so if you would like to keep them the same for the complete dataset, you may need to align and optimize the dataset using single calibration group and after that manually split the groups and perform the Reflectance Calibration operation.