As it is already reflected in the previous GSTR 2A credit cannot be denied. Although if and when notice comes the facts of the case needs to be substantiated. (Show 2 months ITC reconciliation - books vs GSTR 2A).
As GSTR 2A is a dynamic return this issue arises. In the new returns ANX2 all details uploaded for the month after 10th will appear in the next month return so ITC for a period will be clear.
Alternatively you can write to the department that such credits are being claimed as all conditions are being satisfied and request a response if any discrepancies are there.
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