Is there a reason why you don't work directly on the hashrefs ?

use Data::Dumper;

my %x = ("a"  => "red");
my %y = ("b"  => "green");

modifyHash( \(%x, %y) );

sub modifyHash
{
  my ($x, $y) = @_;
  $x->{a} = "circle";
  $x->{b} = "square";
}

print Dumper ( \(%x, %y) );
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Maybe you can avoid having separate hashes in the first place :

use Data::Dumper;

my %coords = (
  x => { a => "Red" },
  y => { b => "Green" }
);

modifyHash(\%coords);

sub modifyHash
{
  my ($c,) = @_;
  $c->{x}{a} = "circle";
  $c->{y}{b} = "square";
}

print Dumper \%coords;
[download]