if you do not want to alter the original hashes, then you must make copies of them before deleting. e.g.:

> perl -wMstrict -e
"my $hashrefA = {};  my $hashrefB = {};
 my ($p, $q, $r, $s) = qw(fee fie foe fum);
 $hashrefA->{$p}{$q} = { qw(a 1 b 2  x 8 y 9) };
 $hashrefB->{$r}{$s} = { qw(c 3 d 4  x 6 y 7) };
 my %Apq_not_in_Brs = %{ $hashrefA->{$p}{$q} };
 delete @Apq_not_in_Brs{ keys %{ $hashrefB->{$r}{fum} } };
 my %Brs_not_in_Apq = %{ $hashrefB->{$r}{$s} };
 delete @Brs_not_in_Apq{ keys %{ $hashrefA->{fee}{$q} } };
 print qq(Apq not in Brs: @{[ keys %Apq_not_in_Brs ]} \n);
 print qq(Brs not in Apq: @{[ keys %Brs_not_in_Apq ]} \n);
"
Apq not in Brs: a b
Brs not in Apq: c d
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also: please give the monks a break and read and follow the Writeup Formatting Tips; the markup you're using is not doing what you seem to expect.