Pradeep,
Goto in IMG, go to the partner function that is assigned to the account group of your customer and check if the ‘Not Modifiable’ flag is checked against the partner function you are trying to delete. If so uncheck the same and save it. (SPRO>SD>Basic Functions>Partner deter> Set up for Customer Master)
Now goto your customer master and select the partner and click on the delete row at the bottom. This will delete the corresponding partner.
Also, in VOPA make sure the 'not changeable' flag is unchecked for your customer master partner procedure.
I am not sure about the above suggestion but I was able to delete and save the customer without any issues.
Thanks,
Ravin
