Your case appears stronger on facts than the Department's proposition. Here, there was no shortage of stock, no unaccounted removal, and no separate allegation of clandestine supply. GST was deposited through DRC-03 during the search on the entire book stock of raw materials and finished goods, the goods were thereafter released by the Department, and the same inventory was subsequently sold in the ordinary course of business.
The sales were duly disclosed in GSTR-1 and recorded in the books. The dispute arises only because tax paid earlier through DRC-03 was not again discharged through GSTR-3B to avoid duplication. If the assessee can establish through stock registers, inventory records, release orders, sales invoices and quantitative reconciliation that the goods sold were part of the very stock on which tax had already been paid during search, a second levy would amount to collection of tax twice on the same taxable value.
The Department's suggestion that the assessee should first seek refund of the DRC-03 payment and then pay tax again on sale is legally cumbersome and contrary to the settled principle that taxes already paid must be appropriately adjusted against the ultimate liability rather than collected twice. The real issue is therefore not whether tax is payable on sale, but whether credit/adjustment of the tax already deposited through DRC-03 must be granted.
The Department may, however, contend that GST paid during search was on "excess/undisclosed stock" whereas GST on subsequent sale arises from a distinct taxable event, namely supply under Section 9 of the CGST Act. Therefore, the burden lies on the assessee to prove the identity and nexus of the goods. Since the inventory consists of books (finished goods) and not fungible raw materials consumed in manufacture, this burden is comparatively easier to discharge through title-wise stock records, warehouse registers, release memos and invoice-wise movement statements.
Reliance may be placed on the constitutional principle against unauthorized double collection under Article 265 and on the broader ratio of decisions such as Mafatlal Industries Ltd. v. Union of India - 1996 (12) TMI 50 - SUPREME COURT, CCE v. Narmada Chematur Pharmaceuticals Ltd. and CIT v. Excel Industries Ltd., which recognize that the Revenue cannot retain taxes beyond what is lawfully due.