The record refund link inside the GST Centre can only be applied to a previously lodged BAS . In order to record that refund/payment against a previous BAS period, you have to first find the previously lodged BAS the GST Centre and then select the  Record Payment  option in the  Action  column.  
  1. Go to the GST Centre from the left-hand menu.
  2. Click Record Payment in the Action column for the BAS period you wish to record the refund against.
  3. Change the radio button option to Refund.  
  4. Select the date of the refund and the account the refund was deposited to.
  5. Input the amount of the payment and any memo for the transaction.
  6. Click the Save button.

How to Record a Refund when you don't lodge your BAS through the GST Centre:

To record a refund when you dont lodge your BAS through the GST centre, follow the steps below: 
  1. Select Gear Icon in the top right-hand corner 
  2. Select Journal Entry 
  3. Line 1 & 2 will be your BAS Liabilities Payable account 
  4. Debit the amount you Collected on GST 
  5. Credit the amount you Paid on GST
  6. Line 3 will be your BAS Suspense (or clearing account you use) enter the required amount on the debit side
See picture attached for a visual on how this manual journal entry should be entered.

User-added image
Please Note: Amounts in the picture are an example only.  6992