If you are using Average Cost, Negative Adjustment will take the average cost on the day the negative adjustment is valued (based on posting date and valuation date).
For example, when you do a Negative Adjustment in Item Journal, Navision will default the unit cost with the Unit Cost from Item Card. It doesn't matter whether you accept the default cost suggested by Navision or change the unit cost to other cost, because the Adjust Cost - Item Entries batch job or the automatic cost adjustment function will adjust the unit cost back to the average cost based on the valuation date. Therefore, no matter what cost you put in the Item Journal during Negative Adjustment will not affect the cost used in the negative adjustment.
If you are using Standard Cost, the unit cost in Item Journal will be defaulted to Unit Cost in Item Card, which is the current standard cost. Later, when the adjust cost function is executed, the unit cost posted by the negative adjustment will be adjusted to the unit cost of the positive entry which the negative adjustment is applied to. Let's consider the following example,
Jan 01, 2008 - Item A is created and standard cost is set to $10.
Jan 02, 2008 - Purrchase 10 units of Item A with $10.
Feb 01, 2008 - Change standard cost of Item A to $12.
Feb 05, 2008 - Purchase 10 units of Item A with $12.
Feb 07, 2008 - Negative 2 units of Item A.
So, on Feb 07 2008, when 2 units of Item A is entered into the Item Journal, Navision will default the unit cost to $12. Accept the cost and post the Negative Adjustment. The Negative Adjustment will be posted with $12. You can verify this by checking the Item Ledger Entries and Value Entries. Now, run the Adjust Cost - Item Entries batch job. After the Adjust Cost batch job completed successfully, check the Item Ledger Entries and Value Entries again. You should be able to see an adjustment entry with -$2 has been added to the Value Entries table to adjust the unit cost to $10.
The Negative Adjustment will take $10 instead of $12 as unit cost because the negative adjustment entry has been applied to the purchase entry created on Jan 02 2008, which is $10.