Read your index file into a hash:

open my $idx, '<', 'index.file' or die "Can't open 'index.file' for re
+ading: $!";
my %index;
while (<$idx>){
    chomp;
    $index{$_} = 1;
}
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And then go through your data file, and replace as needed while copying to a temporary file:

while (<$in>) {
    if ($index{$.}){
        s/foo/bar/g;
    }
    print $tmp $_;
}
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When you're done, override the data file with the temporary file.