Pagination throws 404 error on custom taxonomy archive pages

This function fixed the issue:

function change_posttype() {
  if( is_archive() && !is_admin() ) {
    set_query_var( 'post_type', array( 'post', 'portfolio' ) );
  }
}
add_action( 'parse_query', 'change_posttype' );

Then I just removed the paged and query_string function in my code and just left the regular loop 🙂

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