So after reading through the codex, I came across the pre_get_posts
hook, and I decided to try changing the query with it, which worked for me. Not sure if it is the best way though.
For anyone that is interested here is what I did:
add_action('pre_get_posts', 'get_grandchildren' );
function get_grandchildren() {
if ( isset( $_GET['child_of'] ) ) {
//Make a custom loop which selects the id of grandchildren of parents and puts them in an array and then
set_query_var('post__in', $childrenArray );
}
}