Hi Dave,
Thanks for the response.
Problem is the whole creating of import declaration is happening in GTS. We're not giving any input from ECC other then the Purchase Order. So the partner function value is also getting assigned in GTS.
At least that's what my functional consultant told me. I'm an ABAPer and totally new to GTS. 
If that is true, should we not investigate in GTS itself? The BADI and User-Exit you mentioned are from ECC.
Please correct me if I'm wrong.
Thanks,
Sarif