I am ilfting over SNV calls from hg38 to hg19 using rtracklayer. The liftover result has less number of lines that my input. How do i figure out which SNV calls failed liftover?

liftOver() yields a GRangesList, with one element per input range. I'm not sure what you mean by "lines" but I guess you are unlisting the result and writing it to a file. Instead of unlisting, you can just look at the lengths() of the return value to determine the degree of mapping for each input range.