The "Reset Store Inventory" feature will allow you to reset the inventory balance of a store to zero.
To find this tool navigate to Settings >> General Setting Section > Click on Reset Store Inventory.
As shown on the screen below.
"Reset Store Inventory" pop-up window will appear where you can choose the store for which you want to set the inventory balance to zero.
Once you have selected the store click on the "Zero Inventory" button.
After clicking on the "Zero Inventory" button, another window pop-up will appear, click "ok" to proceed.
Note that the process may take from few seconds to some minutes depending on how big is your inventory.