I found a solution here:
Custom post types, taxonomies, and permalinks
TheDeadMedic’s solution worked like a charm.
function filter_post_type_link($link, $post)
{
if ($post->post_type != 'project')
return $link;
if ($cats = get_the_terms($post->ID, 'project_categories'))
$link = str_replace('%project_categories%', array_pop($cats)->slug, $link);
return $link;
}
add_filter('post_type_link', 'filter_post_type_link', 10, 2);
This checks to see what Project Categories are associated with the project, and uses the first one to build out the permalink for the Project.
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