Could not submit timely response to income tax intimation u/s 143(1)(a)

I received Income Tax intimation about income mismatch between form 26AS and filed ITR. I had responded to it explaining the deductions under HRA Sec 10(13A), Leave encashment on termination Sec 10(10AA) , Allowance for official expenditure Sec10(14) and Professional Tax under section 16.

But I received another communication stating :

With respect to the above inconsistencies, the CPC has examined your response and found it to be unacceptable and thus the inconsistencies remain unexplained.
You are herewith afforded another opportunity to rectify the inconsistencies, by providing an accurate response through online mode within a period of 30 days from the receipt of this communication.

I did not see this email and didn't respond within 30 days. What can be done in this scenario ? How do I get the refund amount for my deductions?