use Data::Dumper;

my %orig = (
  'abc,def' => {
    ',,,item4' => 1,
    'item1,,,' => 1,
    ',item2,,' => 1,
  },
  'kln,mno' => {
    ',,,item4' => 1,
    'item1,,,' => 1,
  },
);

my %new;
foreach my $top ( keys %orig ) {
  push @{$new{$top}}, $_ for keys %{$orig{$top}};
}
print Dumper \%new;