Dear Querist,
W.r.t. factual position point by you in post Serial No. 4 above, I am presuming that said adjustment was done by you on your own, voluntarily and without being pointed out / detected by dept (i.e. other than as a result of scrutiny, audit, inspection or enforcement activity by the tax authorities). It is further presumed that all these adjustments were done prior to furnishing relevant annual return/s.
Dept. may argue that such adjustments are done beyond time-limits prescribed u/s 39(9) and hence, same is not acceptable. For the point of making counter-argument, please note the followings:
A. Before substitution vide Finance Act, 2022w.e.f. 01-10-2022, Said Section 39(9) reads as follows:
"Subject to the provisions of sections 37 and 38, if any registered person after furnishing a return under sub-section (1) or sub-section (2) or sub-section (3) or sub-section (4) or sub-section (5) discovers any omission or incorrect particulars therein, other than as a result of scrutiny, audit, inspection or enforcement activity by the tax authorities, he shall rectify such omission or incorrect particulars 5[in such form and manner as may be perscribed], subject to payment of interest under this Act:
Provided that no such rectification of any omission or incorrect particulars shall be allowed after the due date for furnishing of return for the month of September or second quarter following 6[the end of the financial year to which such details pertain], or the actual date of furnishing of relevant annual return, whichever is earlier."
A1. The words from above provision (i.e. "Subject to the provisions of sections 37 and 38, if") were substituted with the word 'Where' vide Finance Act, 2022w.e.f. 01-10-2022
B. As you are aware, facility of filing Form GSTR-2u/s 38 and matching u/s 43 etc. were never made to a tax-payer.
B1. In these circumstances read with reading of Section 39 (9) (i.e. to a period prior to substitution vide Finance Act, 2022 w.e.f. 01-10-2022), one can argue that as facility to file Form GSTR-2u/s 38 was never made operational and as Section 39(9) started was 'Subject to the provisions of sections 37 and 38', time-limit prescribed u/s 39(9) for adjustments done by you was NOT applicable.
C. Please note that these are just some of counter-arguments.
D. Looking at the stakes involved and there is definitely some risk on solely relying on proving rightness of adjustments as done by you (which may get denied by dept / court etc), you should look for lesser risky alternatives.
D1. Please also check possibility of claiming refund of excess paid taxes on 20.07.2020 (using Covid-related extended date for claiming refund, which will lapse sometime in future if you continue defending the adjustment done till date, which may lead to double trouble for the tax-payer) while simultaneously paying short paid liability of FY 18-19 with interest & penalty.
D2. It is better to involve a local GST professional expert who is operating on the field at your place in such matters.
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.