The easy way would be to use the aliasing of @_:

...
    elsif ( ref($data) eq '' ) {
        $_[0] = $subref->($data);
    }
...
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... but that will of course break as soon as you change the order or arguments of change_all_elements.

The other approach would be to rewrite your code so that it does the assignment and check one level higher:

...
    if ( ref($data) eq 'HASH' ) {
        for my $k ( keys %$data ) {
            if( ref $data->{$k} ) {
                change_all_elements( $data->{$k}, $subref );
            } else {
                $data->{$k} = subref->($data->{$k});
            }
        }
    }
...
# and the same for arrays
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