I figured out the solution to my question of merging two SKUs costs into one. I created a Clearing Asset account. I adjusted quantity of A to zero by moving it's value to this Clearing Asset. That now has my value and the quantity of A is gone. Next I find invoice for B that was already paid and increase it's rate by the merged rate of A and B but in Services field of invoice I reduce this invoice to the original invoiced amount and use Clearing Asset as account to post the negative amount from. As a result, Clearing asset goes down by the merged value, invoice showing correct AP as paid and my B COGS are the sum of A and B on books. Done.