Any stock which is no longer present (transferred to another warehouse / sold / whatever) and then import costs are applied will result in the costs being applied to the Cost Of Goods Variance account instead of adjusting the inventory value account.
Ideally you probably want to leave the stock there, and anything else wanting stock to omit that stock for selection. That's not practical to implement, however as there are many places you'd have to touch to intercept the stock selection because we don't have a single, unified way of selecting / taking stock.
Personally, I'd like to re-do aspects of our stock system to allow reservations of stock - stock comes in, and anything wanting stock to indicate it wants x quantity of a product, but not actually take the stock until a picking phase - that way things would make more sense than our current method of reservation being actually reducing the stock quantity which is silly because you don't know always which stock quantities you are going to take, you just know you want to put aside a quantity.
Having said that, I still have not answered your question - right now I don't have a good answer, the best I can give is my first suggestion which might be - as I said - impractical to implement.
You should perhaps ask the question of our crack support team - but not in forums because they don't engage here in forums - lodge a request on our
helpdesk.
Mike