problems getting output from watershed inlet points

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Hello SWAT Users!

I want to discuss with you concept behind adding inlets of draining watershed in Arc SWAT Project. First I have added inlets of draining watershed and then after completing other process for e.g., HRU, Weather generator, writing input files, later I have added discharge data to specified watershed containing inlets. After that I rewrote the input files and ran the model by using two methods a) with and b) without adding inlets to watershed. I have compared the outputs from both ways and found that the contribution from subbasin containing inlets is less as compared to when I do not add inlets. May be Arc SWAT model did not read the discharge data that I have inputted to model. What could be the possible causes? Please guide me with your valuable suggestions. SWAT Flow out file with and without inlets is attached along with this query.

Kind Regards:

Adnan