Revenue is expected to treat payment of taxes made in June, 19 as wrong / excess payment of taxes and deny the taxpayer the benefit of earlier quoted provisions (including denial of relief from from interest-liability).
Assuming that extended date of claiming refund, using covid-related extensions granted by SC, is also not available in given case, following can be done:
A. Pay taxes under IGST, against Dept's observation / objection, wherein the fact that tax-payer has considered very same supply as 'Intra-state' and paid taxes under CGST & SGST - while filing return in from GSTR-3B - should be brought clearly on record of Dept.
B. Seek benefit of Section 77 of CGST Act, 2017 read with Rule 89(1A) & Circular No. 162/18/2021 dt. 25.09.2021 and claim refund of earlier taxes so paid in June, 2019.
C. If Dept. proposes rejection of refund-claim so sought (as feared, for reasons briefly mentioned in my earlier post)), kindly submit reply to such SCN by taking - very broadly specking - following two grounds:
1. Your disclosure of very same same as 'intra-state' while filing form GSTR-3B, which is now treated as inter-state by Dept. while demanding IGST, itself means that you have duly & fully fulfilled conditions to seek benefit of Section 77 read with Rule 89 (1A).
2. Alternatively and without prejudice to above, payment made by the tax-payer in June, 19 cannot be treated as 'wrong / excess payment of taxes' at all (i.e. same are only amount deposited / paid in name of taxes but same was NOT tax-payment per se). With suitable evidence/s like CA certificate, you can prove that those taxes were never charged & recovered from any one and burden there-against was never passed on anyone (Plus, you have already paid taxes i.e. IGST, as charged & recovered).
3. And there is no time-limit applicable for claiming refund for such deposits / payments and Govt. cannot keep such amounts with itself as taxes without any authority of law. You can quote multiple HC rulings which are favouring tax-payer in this regard.
4. But, please be mindful of Nine member Bench of Supreme Court's decision in case of Mafatlal Industries v. Union of India, to understand the risks involved.
Also, there is option of filing writ petition once SCN is issued proposing denial of refund in given set of facts.
These are broad guidelines only. One needs to be careful while replying to objections of Dept., while paying taxes under correct head, while seeking refund and reply to SCN proposing denial of refund (where reply needs to be suitably fine-turned, based on actual allegations / charge against the tax-payer) etc.
This can be long-drawn legal battle where when tax-payer is not paying interest seeking benefit of Section 77 (2) & Dept. starting separate proceedings u/s 73 / 74 for non-payment of taxes (though duly charged & collected in June, 19). And same needs also be separately defended seeking benefit of Section 77 as well as non-applicability of Section 74 (if same section is indeed used) for given set of facts & circumstances.
Last but not the least, one need to take the quantum involved in given case & associated issues on practical side, before embarking on journey of seeking justice.
All said & done, what tax-payer has done here is a default of very technical nature with zero gains. And this is fit case where Govt / CBIC must comes with suitable clarification / instructions to their officers by taking holistic view favouring such tax-payers.
But till then, this can be long-battle, though I sincerely hope that officer takes holistic view and grant the tax-payer benefit of Section 77 read with rule 89 (1A).
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.