Hi Charan,
This sounds like a nightmare :( Is there any way you can get the sender to verify this with FedEx? It's annoying, but it might save you this ridiculously high import fee. You can maybe also offer to show an invoice from this transaction (hopefully you haven't cancelled it yet...) to prove your point (i.e. the same addresses, same $ being declared, etc.).
Those are the only things I can think of right now, but I really hope this gets resolved for you in a fair manner!