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;
}
}