Almost exactly what I wrote...

How do you like this version? ;-)

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;
for ( [ grep { $count!=$count{$_} } map { ++$count{$_};$_ } map { keys
+ %{$HoH{$_}} } keys %HoH ] ) {
     foreach my $hash (values %HoH) {
         delete(@$hash{@$_});
    }
}

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