if you have that many lines, are you sure you want exactly 1% or a statistical estimate would be enough?
In that second case, just randomize at 1% at each line...
awk 'BEGIN {srand()} !/^$/ { if (rand() <= .01) print $0}'
If you'd like the header line plus a random sample of lines after, use:
awk 'BEGIN {srand()} !/^$/ { if (rand() <= .01 || FNR==1) print $0}'
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