venu,
This is more of a business related question. What will happen in SAP is just "noting" the business decision.
Two things are important -
1.What are the rules in the contract, between the buyer and seller; between the seller and the freight forwarder (transporter).
2. Is this a big customer? and does the seller want to please the buyer?
Don't focus on what will be done in SAP i.e. credit note or debit note or return or....
Contact a senior manager (Electronic company) and ask, this is a situation - what would be your approach?
Note: As a senior executive in India, their way of dealing could be different from how it is done in other parts of the world.
Typewriter