Dear Sir,
Query-wise my reply is as under:-
Reply to Q.No.1 :
Filing reply to SCN via email amounts to not filing reply. The department is right on this point but at the same time the opportunity for personal hearing is statutorily required. In spite of non-filing of reply to SCN, the refund claim cannot be rejected without personal hearing. It is against the principles of natural justice. This will be one of grounds of appeal in this case.
Reply to Q.No.2 :
While filing appeal you should mention the refund of amount rejected but you should mention the correct amount within bracket and explain the factual in the 'brief facts of the case' as well as in the grounds of appeal. It is a calculation mistake and you are not going beyond the issue by way of claiming correct amount of refund claim.It is your right to claim correct amount at appellate stage.
It is worthwhile to mention that in one of my client's case, the party forgot to claim small scale exemption of ₹ 10 lakhs (Threshold exemption service tax) in the reply to SCN and also in the case of personal hearing. This new point was raised before the Commissioner (Appeals). The Commissioner (Appeals) allowed the benefit of threshold exemption of ₹ 8 lakhs on which ST of ₹ 96,000/- Approx. was involved. The party got the refund of ₹ 96,000/- and accordingly penalty and interest were also reduced. It was in the interest of natural justice. It was additional point raised before the Commissioner (Appeals). At that time small scale exemption of ₹ 8 lakhs was admissible.
So in my view, you must fight for correct amount.