I assume you are referring to an Assembly Item marked as phantom. If this is the case then the only thing I can think of is to post an inventory adjustment for Qty 1 at the cost you want. The average cost is only calculated when a transaction positively effecting inventory is posted. NetSuite then calculates the average cost of on hand qty at that time
For LPP it is similar. NetSuite needs a transaction to base it off of
Because the item is phantom a transaction will never be posted to it unless you make one up like an Inv Adj