When closing Work Orders that do not have any inventory quantity, the costs do not transfer to COGS.  They continue to show up in Net WIP.  Every month, I must do GJ entries to transfer these amounts to COGS.
 
(I say yes to rebuild summarized costs, when asked)

If there is no quantity to go to stock, then the question about the final quantity is meaningless.  Are you closing them in WO-J?  Or doing a 0 quantity FP in WO-I?  The residual cost should be transferred to WIP Variance when the WO is closed unless it is a Status I (Indorect) WO.