Add specific members-only categories back to main loop when filtering searches and archives.

my_pmpro_category_filter.php

<?php
function my_pmpro_category_filter($query)
{
	//get the members-only hidden categories
	$hidden_cat_ids = $query->query_vars['category__not_in'];
	
	//set the members-only category IDs NOT to filter
	$not_hidden_cat_ids = array('1','10');

	//add hidden category IDs back to the query
	foreach($not_hidden_cat_ids as $not_hidden_cat_id)
	{
		if(($key = array_search($not_hidden_cat_id, $hidden_cat_ids)) !== false) {
			unset($hidden_cat_ids[$key]);
		}
	}
	
	//set the updated hidden category IDs
	$query->set('category__not_in', $hidden_cat_ids);
}
$filterqueries = pmpro_getOption("filterqueries");
if(!empty($filterqueries))
	add_filter( 'pre_get_posts', 'my_pmpro_category_filter');

This gist no longer works with PMPro 3.0+. You can find an updated version of this gist here: https://gist.github.com/ideadude/4ebc6abe1c88bd1a38198a60b883eea9