That sounds like eBay's boilerplate for a chargeback case. In practicality it is impossible for the seller to provide evidence of what the buyer actually received, because as you say the item could have been opened by customs or postal services in between.
I am not sure what you can do about this to get a successful outcome. One option is to reply to the case saying you are willing to offer the buyer a refund if they will return the (partially received) item first. You would need to be willing to purchase and attach a postage label for them to return the item to you at your cost. If the buyer's bank or card provider is willing to accept that as a reasonable next step, then you might force the buyer to do that or go away. If you believe that the buyer is trying to commit fraud then that might make them give up.
