There are two ways to fix inventory stock quantities depending on whether you want to fix the stock quantities for one item or for all items.
1) Edit Item
2) Select the item where you want to fix the stock quantities.
3) Go to the Cost/Stock Levels tab
4) Enter Supervisor Override Mode
5) Right Click on the Cost & Stock Levels grid
6) Select Fix Quantities
7) Exit Supervisor Override Mode
The link below demonstrates this Fix Quantity feature:
1) Go to Inventory Reports > Inventory Integrity
2) In the Settings tab, check the Fix Inventory Stock Quantities
3) Click Run Checks button
The link below will demonstrate how to fix inventory quantities for many inventory items.