Duplicates When using Nested WP_Query

Never mind, I got it.

For anyone who may run into a similar issue. See below.

Main Loop:

if ( $the_query->have_posts() ) {
    while ( $the_query->have_posts() ) {
        unset($do_not_duplicate);
        $the_query->the_post();
    }
}

Secondary Loop:

if ( $projects_query->have_posts() ) {
    while ( $projects_query->have_posts() ) {
        $do_not_duplicate[] = get_the_ID();
        if( in_array( get_the_ID(), $do_not_duplicate) ) 
            continue;
    }
}