Hi,
This is quite a problem when running SWAT-CUP and then transfer it to SWAT (ArcSWAT/QSWAT) again.
My recomendation is to take the best_par, use those to run SWAT-CUP again, but only once; doing that, you are making sure that your TxtInOut (those hundreds/thousands of txt files are your SWAT model inputs) have the proper best_par values that yielded your desired NSE.
Now, a usual warning: you need to double check (even triple check) if the swat.exe version of SWAT-CUP and your SWAT (ArcSWAT/QSWAT) are the same, if not, that could be a great problem. For example, if your swat.exe from SWAT-CUP is ver 601, and your SWAT (
ArcSWAT/QSWAT ) is ver 695, then that is a major redflag; because of the big version difference in which some equations were updated/corrected.
After doing that, you should be able to get the same results of your project in both
SWAT-CUP and
ArcSWAT/QSWAT.
Regards,
Oscar M Cabezas-Nivin