The quantity on hand of your products is automatically calculated based off of the total quantity you have in each warehouse assigned for your product.
For example, if you have have two warehouses Warehouse A and Warehouse B, with a quantity of 4 at A and a quantity of 3 at B. Your total quantity on hand for the product would be 7 in this case.
If you do not want a specific warehouse's quantity to be included in the sync balance you can un-check the checkbox to include quantity in sync balance. For example, if you do not want warehouse A's balance to be included in the sync you can un-check the setting and we will only sync warehouse B's quantity of 3. Your total quantity on hand will then show as 3 for this product.