If you do not export/import the Unit Cost field with a Physical Inventory, this value will be defaulted from the item master. It calculates the appropriate unit cost to do exactly as you describe (losing the cost with the item), and deals with the scenario if there are multiple costing lots with different average values, just like if you shipped the same qty as is being lost.
You should not have to change the Unit Cost value unless you want to add/subtract a different amount than as described above.
You should be aware that costs are not stored by location in Adagio Inventory, so if you use FIFO/LIFO costing and have multiple costing lots, they do not necessarily relate to particular loations. So if you create 4 physical inventory worksheets, the costs are determined only if there is a different in the physical count and at the time they are imported.
If you post a stock count loss, it will be costed as if the qty was shipped. There is no place to identify a specific costing lot, should more than one be in use. If you want to remove qty and cost from a specific costing lot, you should use the Adjustments function and not Physical Inventory.
Also, when a Physical Inventory is imported, the quantities and costs are not yet updated - you still have to post it. This means that if the results of the import are not what you expected, nothing bad has happened yet to your data. You can print the phys inventory report, make changes, or re-import a corrected file if required. Definitely make a backup before Posting!
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Regards,
Softrak Tech Support