Needless to say that Dept's views are - almost surely - expected to be unfavourable from point of view the tax-payer in given situation. Issues raised is subject to different interpretations, complex in nature and will be ultimately settled by higher courts one way or other.
With above caveats, my views are as under:
A. Section 142 (9) (b) of the CGST Act, 2017 is not applicable in given situation. This is because, in my view, pursuant to filing of revised return, CENVAT credit is NOT found to be admissible to such assessee. Credit of Rs. 7.25 crores was admissible to the assessee whether he files return (including revised return) or not in given situation.
B. I read the restrictions of first proviso to Section 140 (8) in light of my above-reading of Section 142 (9) (b). In other words, restrictions of first proviso to Section 140 (8) does not apply to the given situation in my view.
C. (Though one HC has ruled otherwise in the context of Credit of KCC, if I remember correctly), the difference between Section 140 (1) & 140 (8) - w.r.t. filing of revised return - also needs to be kept in mind, while defending oneself.
Furthermore, kindly note that if 'Section 142 (9) (b) of the CGST Act, 2017 is said to be applicable in given situation', I hold a view that there is no time limit prescribed to claim refund of resultant additional Cenvat Credit' either under section 11B of the Central Excise Act, 1944 (1 of 1944.) or under GST Act, 2017.
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.