Penalty inspite of reversal of excess claimed ITC - Goods and Services Tax - GST

Dear friends, One of my client claimed excess ITC of Rs. 40 Lacs in the month of Jan.2018 (due to typo error). ITC reversed in 3B of Oct, 2018. The fact of reversal was also mentioned in GSTR-9 table No 12. After assessment order Int u/s 50 for the utilisation out of this excess ITC availed Rs.15000 deposited through DRC-03 . Penalty of Rs. 4 Lacs imposed u/s 122(2)(a) (10% of Rs. 40 Lacs) My point is that Section 73 (9) says... The proper officer shall, after considering the representation, if any, made by person chargeable with tax, determine the amount of tax, interest and a penalty equivalent to ten per cent. of tax or ten thousand rupees, whichever is higher, due from such person and issue an order. [See Rule 142(4) ] in my case tax determined should be treated as Nil as the tax was paid in 3B itself GSTR-9 also filed that is well before issuing the SCN, however in the assessment order it was mentioned that as the amount of Rs. 40 Lacs has already been reversed in 3B,I appropriate the same in to the government account that means whether tax determined to be treated as 40 Lacs? Plz guide whether penalty of Rs. 4 Lacs u/s 122(2)(a) is valid?