GST applicable will be recovered with benefit of ITC available only to the limited extent of the time available within section 16(4) when this mistake is realized. There is no estoppel that ITC must be availed because claim of credit is through the return filed under section 39 (section 16(2) refers) and not from the receipt of tax paid supplies.
(ICAI FAQ PUBLICATION 06-09-2017 EXEMPTION: FAQ NO. 9)