Just to get a bit more obscure...

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

my %HoH = (
        elt1 => {
                A      => "ccc",
                B       => "ccc",
                C       => "ccc",
        },
        elt2     => {
                A      => "ccc",
                C      => "ccc",
                D      => "ccc",
                B       => "ccc",
        },
        elt3    => {
                A      => "ccc",
                E      => "ccc",
                C      => "ccc",
        },
);
 
my %count;
my $count= scalar keys %HoH;
my $k= [grep {$count==++$count{$_}} map {keys %{$HoH{$_}}} keys %HoH];
foreach my $h (values %HoH) {
    %$h= map {$_,$h->{$_}} @$k;
}

use Data::Dumper;
print Dumper(\%HoH);
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