To auto reconcile a completed stock take:

Step 1: Visit Inventory > Stock Takes.
Step 2: Go to the Completed section.
Step 3: Click the Open button against the stock take to be reconciled and do the due diligence at your location to account for any discrepancies between counted and theoretical stock.
Step 4: Once done, click the checkbox against the items you want to reconcile under the Auto Reconciled column and click the Auto Reconcile button.