With regards to concerns raised by the Querist vide Post No. 3, my views are as under:
1. Due to reason explained in earlier post, if there is no wrong availment of ITC, there is no question of any offense by the buyer. Hence, question of coercive action like arrest should not ideally arise.
2. Even otherwise, contravention of 'taking ITC after time-limit prescribed u/s 16 (4)' per se does not fall within offenses listed in 'clause (a) or clause (b) or clause (c) or clause (d) of sub-section (1) of section 132 which is punishable under clause (i) or (ii) of sub-section (1), or sub-section (2) of the said section'. Hence, power to arrest available under Section 69 - should not ideally come into picture.
3. But, querist should submit proper replies with all grounds to Dept. explaining its legal stand and reasoning, including (and only if threat of arrest is genuine / real) why no offenses - as listed above - attract present scenarios.
4. If fear of arrest still persist, it would be better if it approaches & meet senior officer including jurisdictional Commissioner and explain its position in person.
5. All this should ideally eliminate threat of arrest. If still not (a highly unlikely scenario), the querist needs to consider approaching court either seeking anticipatory bail or High court seeking action against denial of ITC in GSTR-2A by GST portal when law does not support such action.
All above should be treated as strictly personal views of mine only and not as a professional advice or suggestion.