Maybe you could avoid the regex approach and use split and join?

#  untested
my @parts = split /-/, $input;
my $first = shift @parts;
my $last  = pop @parts;

my $reassembled;

# then
$reassembled = $first . '-' . join ('_', @parts) . '-' . $last;
#  or something like this 
$reassembled = join '_', @parts;
$reassembled = join '-', ($first, $reassembled, $last);
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The above assumes no CSV type quoting issues with embedded separators, for which a proper CSV parser like Text::CSV is needed.