Penalty u/s 271A

Hey.This is regarding my friends taxability.Income is below BEL.He is a doctor employed by a hospital.He received Professional Income as TDS u/s 194J gets deducted.His Income for F.Y-2015-16 was Rs 1,90,000.He filed return of Income claiming refund of Rs.19000.But he did not maintain BOAs and selected the option NO in the Income tax Form.Now he received a defective notice stating that Balance Sheet and P/L Must be filed and any changes done apart from B/S AND P/L,will render the Return Invalid.He did not file Return u/s 139(9),as he had to change one field in the ITR Form of Sec 44AA(making it yes) .If he would have done that,then his Income Tax Return would have been Invalid(as mentioned in the notice). He drafted this reply to Bangalore CPC. Bangalore CPC said YOUR REPLY HAS NOT BEEN TAKEN INTO CONSIDERATION.Now will he receive Penalty Notice u/s 271A for Rs.25,000 or should he wait for the CPCs further reply?