I would think about reading the change file and creating a hash whose keys are all the lines that have changed, something like this:

if ($info =~ /(\d+)-(\d+)/) {
        $changes{$file}{$_} = 1 foreach ($1..$2)
    } else {
        $changes{$file}{$info} = 1;
    }
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Then, in a separate loop, I'd iterate through the lines in the data file and test each one, something like this:

$line =~ m/~(\d+)~/;
print $line if $changes{$file}{$1};
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