As has been said elsewhere, I don't believe that you can do it as an atomic operation with XML::Simple, but I believe that you could maybe do it in 2 stages e.g. something along the lines of ...

my $ref = XMLin(<file);
my $keys_you_dont_want_re = 'key1|key2|key3|...';
$ref = { map { $ref->{$_} } grep !/^($keys_you_dont_want_re)$/, keys %
+$ref };
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Just a, not especially well considered, thought ...