This article explains the reasons your COGS in QuickBooks Desktop might not match what you see in Point of Sale.
What if I still have an On-Hand QTY for these items?
If you suspect receipts have been deleted or marked as sent, and you are sending detailed transactions to QuickBooks, look at each receipt's Financial History. From Sales History, choose I want to > Show Financial Detail:
There may be times where a bulk item, such as gravel, is received as one type of quantity (for instance, a ton), and then sold as a different quantity (a square yard). If this is occurs, it has serious ramifications for your COGS account.
Choose Inventory > Item to inspect items that may fall under this category. Click Show Details to see the History for each. Make sure Receiving Vouchers and Sales Receipts show reasonable quantities and prices.
If you're in this scenario, a simple general journal entry in QuickBooks can correct the issue. To fix without a journal entry, you will have to reverse and reenter each receipt where the quantity was entered incorrectly.