CRA acknowledges that ITCs identified during a GST audit generally should be deducted in a return assessed by the auditor

Input tax credit claims, if identified on a timely basis, can be claimed in the return for the reporting period in which the GST/HST first became payable or in a subsequent reporting period. However, CRA appears to agree that where, during an audit, a registrant identifies previously unclaimed ITCs, the right course of action in accordance with ETA s. 296(2) is for those ITCs to be deducted in the return being assessed by the auditor (being the first such return in which the ITCs were claimable) rather than being deferred to be claimed in a future return, or being claimed under a request made to CRA to adjust a previously-filed return in accordance with P- 149.

May 2015 CPA Roundtable, GST Q. 12 under ETA s. 296(2).