Under Stock Control, there is a Stocktake tool and a New Stock Adjustment tool.
A Stocktake is done when there is a need to change the quantity of stock, without changing the Moving Average Cost (MAC). If you are conducting a regular stocktake for your business, use the Stocktake tool. You can do a Stocktake by following the instructions here.
On the other hand, if there is an adjustment to your inventory that affects your MAC, such as having damaged goods, promotional goods, or new products, using the New Stock Adjustment tool is the right option to update the inventory and changes in cost. You can make a New Stock Adjustment by following the instructions here.
For more details on Moving Average Cost (MAC) and how to calculate it, you can watch the video here.
Scenario 1:
Your QuickBooks Commerce account indicates that you have 25, medium-sized, White T-shirts, in stock. When you go to the warehouse to do a physical stocktake, you realize that there are only 23 in stock, and there is no reason for the discrepancy. Don't worry, this happens. But what should you do to adjust your stock levels in this case?
Question: Do you do a Stocktake or a New Stock Adjustment?
Answer: Use the Stocktake tool. The Moving Average Cost (MAC) should only be recalculated when there is a known adjustment to the stock levels i.e. when a purchase order is created or stock levels change due to products being returned etc. If the reason for the change in stock levels is unknown, recalculating the MAC will render it inaccurate. Therefore, the Stocktake tool is the right option, as it does not affect the MAC.
Scenario 2:
During a stocktake, you realize that a total of 5 Cat Bowls (Purple) were damaged. You want to change the quantity of the product and account for the loss in QuickBooks Commerce .
Question: Do you do a Stocktake or New Stock Adjustment?
Answer: A New Stock Adjustment would detail the changes clearly, including the decrease in quantity and adjustments in cost which ultimately affect the MAC.
After doing a Stocktake or a New Stock Adjustment, you can always view the summary. If you create a Stock Adjustment by accident, you can void it by clicking the Void Stock Adjustment button on the top right-hand corner of the page. 
When you are done editing the information, click Create at the bottom right hand of the page to confirm.
If the reason for doing a New Stock Adjustment falls outside of new products, returns, damaged, or promotional goods, you can add a custom reason for doing a New Stock Adjustment by following the instructions here.