different approach (just idea):

# load files into alias => id pairs:
my $file1 = {
  'bobssite.autossl.net' => 'bobssite',
  ...
};

my $file2 = { ... };

my @different_aliases = grep exists $file1->{$_} and $file1->{$_} ne $
+file2->{$_}, keys %$file2;

delete $file1{keys %$file2};

my @aliases_not_in_file2 = keys %$file1;
my @ids_not_in_file2 = do {
  my %tmp;
  @tmp{values %$file1} = values %$file1;

  keys %tmp;
};
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