Hi!
So if I understand correctly supplying site has reported that they have sent 9 pcs but actually you received 3 pcs? I am not sure what is the site set up but I assume that you have also received invoice for 9 pcs? If shipments are not closed/invoiced you could try to undo the delivery and and correct the delivered qty on the shipment.
In general it is not possible to cancel partially received DO but you can change the qty to move but it can not be less than delivered qty. The issue is that it will try to update the connected PO and CO and you will get and error because the connected CO on supplying site is closed.
If undoing shipment will not work I see as only option to receive the qty and then do return to credit and ask for credit invoice from supplying site. They will anyway need to correct their balance.
With the complexity of all of those transactions I just went ahead and “received” the remaining balance and cycle counted the excess out of inventory for the destination site. This was the simplest way I could find.