Currently, if you issue stock (regardless of the costing method used for that item), if you had to return some of that stock from the project, that stock's cost price will represent the average cost of the item. This can cause discrepancies if you were to then either issue out that stock again, or run a valuation on your current stock.
I think the return of stock should use the same costing method for that item as was used whenever the stock was issued. I had recently been made aware of this whenever testing the issuing out of stock to projects where the stock used the actual costing method and dealt in batches. It was returned at the average cost price, when I issued out thar sane batch, the average cost price was used. When I ran a stock valuation, I was able to see that the stock brought in was also using the average costing price.