Hi,
On the Batch Processing window's Validation tab, if the "Serialized Items" check box is set, the on hand quantity is set to equal the count of serial numbers. If this is not happening for you, this is an unexpected result and not something that can be reproduced with other data.
My only suggestion is to ensure that the serialized check box is set on the stock code, delete one of the serial numbers (Inventory - Edit/Query Serial), verify that the on hand quantity is reduced, then validate the serialized items.