If you export/re-import a physical inventory reconciliation, the difference between the 'Stock on hand' and the 'quantity on hand' will be posted as an adjustment, when you run the Post Inventory Reconciliation function after the import.

Alternately if you know the quantity difference already, you can simply import an Adjustment function.

One main different between these 2 processes is that importin g a physical inventory allows you to print a report and otherwise verify that the changes are as desired before you officially post the changes to update the quantity. Importing an adjustment batch immediately updates the quantities (and costs, if selected), so you need to be sure of the values before doing this.

Make a backup of your data before running either of these functions.