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Issues: (i) whether an assessee whose application under the 2017 amnesty scheme was still pending could seek relief under the 2020 amnesty scheme; (ii) whether amounts paid pursuant to judicial orders and interim directions were to be appropriated under Section 91 of the Kerala Value Added Tax Act, 2003 or under the 2020 amnesty scheme; and (iii) whether any excess amount remaining after settlement under the 2020 scheme was refundable.
Issue (i): Whether an assessee whose application under the 2017 amnesty scheme was still pending could seek relief under the 2020 amnesty scheme.
Analysis: Section 10(12) of the Kerala Finance Act, 2020 expressly permits assessees who had earlier opted to settle arrears under the former scheme, but had not completed payment, to opt under the 2020 scheme. The pendency of the earlier amnesty application did not by itself defeat the later application, since the liability had not been finally settled under the earlier scheme.
Conclusion: The assessee was entitled to maintain and pursue the amnesty application under the 2020 scheme.
Issue (ii): Whether amounts paid pursuant to judicial orders and interim directions were to be appropriated under Section 91 of the Kerala Value Added Tax Act, 2003 or under the 2020 amnesty scheme.
Analysis: Section 10(8) of the Kerala Finance Act, 2020 overrides Section 91 of the Kerala Value Added Tax Act, 2003 for payments or deposits made after service of demand notice and directs that such amounts be given credit as tax before computing the arrears under the scheme. The amounts paid by the assessee pursuant to the Supreme Court order, the statutory appeal, and the interim order of the High Court were treated as provisional deposits made in the backdrop of pending litigation and were therefore required to be reckoned under the amnesty scheme rather than under the general appropriation rule in Section 91.
Conclusion: The payments were to be adjusted under the 2020 amnesty scheme and not appropriated under Section 91 of the Kerala Value Added Tax Act, 2003.
Issue (iii): Whether any excess amount remaining after settlement under the 2020 scheme was refundable.
Analysis: Section 10(9) bars refund only of the amount actually settled under the scheme. It does not prohibit refund of any surplus that remains after the scheme computation is completed and the liability is fully settled. Accordingly, if the assessee's remittances exceed the amount payable under the scheme, the excess cannot be retained by the Department merely by invoking the refund bar.
Conclusion: Any excess amount remaining after settlement under the 2020 scheme was refundable to the assessee.
Final Conclusion: The amnesty application had to be processed under the 2020 scheme, the disputed remittances had to be credited under that scheme, and any surplus remaining after full settlement was liable to be returned.
Ratio Decidendi: Where a special amnesty enactment contains a non-obstante crediting provision, payments made after demand notice in the course of pending tax litigation must be reckoned under the scheme rather than under the ordinary appropriation rule, and any amount not absorbed in the final settlement remains refundable as surplus.