Hi, I used CAD for merging datasets during MIR. I faced the same problem. The solution is: the datasets you are trying to merge should have different labels i.e if dataset 1 has labels: F and SigF, dataset 2 should be F_d1 and SigF_d1. Mention the labels during the cad run.
Ramanuj Banerjee Crystallography and molecular Biology Division Saha Institute of Nuclear Physics, Kolkata, INDIA