When we process a returned item through a sales order, sometimes (always?) the COGS shown in the COGS or commission report during SO-G Post Invoices is zero.  No posting is made to inventory or COGS accounts, and the product is given a zero cost in inventory.  We use FIFO costing.
 
Why?
 
How to fix (both after-the-fact and to prevent future occurences)?

If you are processing a return (rather than a void which is tied to a specific original invoice) how would the program know what value to use for a cost?  It really needs to know what the original invoice was.  I believe if you are on Average Cost rather than FIFO or LIFO, it uses the current average but that really isn;t right either.

Longer term, the RMA program under development will be able to identify the original invoice and from that get a cost.  May also have the ability to manually enter a cost.  
 
Short term, you could use IN-C to adjust the $0 part out and then adjust it back in at your chosen cost.  That would update both inventory and the GL.