I have received an intimation of Short Deduction but payment amount is not eligible for TDS as the amount is below the threshold limit. What should I do?

You can file correction statement and raise threshold flag ('Y') in column no. 326 (24Q), column no. 424 (26Q), column no. 729 (27Q) and column no. 680 (27EQ) for 'Reason for no / lower deduction'.