One way, which would be slow for directories with lots of files would be something like this. Sort the array of filenames, then use the pars before the _ as hash keys, the elements just overwrite the previous values.

#!/usr/bin/perl
use strict;
use warnings;

my @data = qw/12345_-v1.pdf 12345_Av1.pdf 123456_-v1.pdf 123456_Av1.pd
+f 123456_Bv1.pdf/;
my %hash;

for my $f (sort @data) {
  my ($key,$version) = split /_/,$f;
  $hash{$key} = $version;
}

for my $key (keys %hash) {
  print $key . '_' . $hash{$key} . "\n";
}
[download]