Hi,
After you have calibrated your model in SWATCUP, use the files modified by SWATCUP as your calibrated model, do not try to change the parameters in ARCSWAT!
Here is an example of why if you need to change one parameter from the default to 0.357493737 (best value in your calibration) if you use arcswat to do it, arcswat will write 0.357 not exactly the same. The situation is even worse if that parameter is a really sensitive one. So it is no advisable to use arcswat to modify it!
To be sure that you are using your calibrated model, ask your swatcup to modify the parameters to their best value and then you have it, your model is calibrated
If you have other questions, contact me by email
Regards
Oscar