Transfer everything you don't physically have into a separate warehouse code.

Only count the "real" warehouse code.

Is it possible to transfer from one warehouse to another through a sales order?

No... but you could write a button script to create the transfer transaction from an SO.

Lot / serial valuations would be more complicated... but basically your shipper would enter the final details, and post the transfer, when things go out the door.

Edit:

Side benefit of the transfer: you have a transaction recording the shipping transaction details, at the time it leaves.

Thanks very much Kevin.