If the carriage returns are right next to each other something like this should work:

use File::Slurp;

my $text = read_file('filename');
$text =~ s/\r\r/\r/g;
print $text;
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Or you might use: $text =~ s/\r+/\r/g; if there could be multiple adjacent blank lines.

Knowing exactly the structure of the file would help. What does od -c filename print out near those blank lines?