Hi BQNick,

While you are able to enter varying amounts when recording BAS payments (such as if you paid the amount in instalments), you will be unable to do the same if the GST Centre is expecting a refund. While it is not possible to revert you to the previous GST Centre, if the amounts you have received don't match the BAS amounts you have recorded in QBO you can use a clearing account to record the payments. You record your bank transactions to this clearing account, then mark the BAS periods as refunded using this balance. This way the BAS refunds are recorded and you will also be able to reconcile your bank account. Firstly, create the clearing account:

1. Select the Settings icon (top right), then Chart of Accounts. 
2. Select the green New button (top right).
3. For both the Account Type and Detail Type, select Cash and cash equivalents. Give the account a name relevant to you (eg Clearing, or Adjustment Account etc) and Save and Close. 

Then you can categorise your bank transactions this account and use the balance to record the refunds in the GST Centre:

1. Select the Banking tab and click on the transaction to expand it.
2. Under the Category dropdown, choose the Clearing or Adjustment account you have created. Select the tax code Out of Scope, then Add. Repeat for any other ATO refunds. 
3.  Select the GST tab and click Record refund on the first BAS period. 
4. From the account dropdown, select the Clearing or Adjustment account you have created. Add a memo as required, then Save. Repeat with any other BAS periods as required. 

Now you have accounted for the transactions in the bank, recorded the refunds in the GST Centre, and will be able to reconcile your bank account. 

-Kass