It appears that the "every" command in gnuplot is what you're looking for:
plot "filename.txt" every ::1000::2000 using 1:2 with lines
Alternatively, pre-process your file to select the rows in which you are interested. For example, using awk:
awk "NR>=1000 && NR<=2000" filename.txt > processed.txt
Then use the resulting "processed.txt" in your existing gnuplot command/script.
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