User should select the appropriate PAYG Option. It's not possible to report both the instalment amount and the varied amount. It says -  OR IF varying T7, complete T8,T9,T4.

If the issues persist, please check:

- If the form IAS is past due? you will not be vary the instalment amount, please contact ATO in such case. 

In case ATO is not able to help, please adjust it at year end.

Question: How to remove the pre-populated info provided by ATO. How do I delete the pre-fill Instalment amount.

Answer: This is ATO side validation. Please see how it can be resolved it based on ATO instructions:

Since it's the second quarter, the formula will be (5000 * 50%) - 3413 = -913. In this formula 5000 is the Estimated tax for the year filled by the user on current form, and 3413 is the Varied amount from the previous quarter.  Since the T9 value -913 is negative you should report 0 at T9. This is why ATO validation says it's incorrect and T9 must be 0. It can be lodged with it. Probably, ATO will automatically recalculate the amount in the next BAS, but not sure 100%.