Reply To Notice

Kindly give your opinion in the following scenario -

Suppose a person X files his return against which he receives a notice of defective return bcz the credits in 26 AS was more than the income shown by him

Now, instead of filling the return u/s 139(9), he revise the return u/s 139(5) correcting the above discrepancy. After that, he receives another notice u/s 143(1) bcz he has claimed deduction u/s 80D more than the allowed limit.

Further, the time period for replying to notice of 143(1) has elapsed.

So now, what should be done. Whether to again revise the return u/s 139(5) or reply to the initial notice u/s 139(9).