Hi Ali,
In addition: Which inventory costing model are you using?
When you post a inventory deduction using an inventory journal, the cost on the line is ignored. It is only used when you post an increase. At a deduction AX will use it's own costing model logic.
Depending on the costing model, you can "mark" transactions (link two inventory transactions) and run a closing or recalculation job to assign to correct cost.