Sorry to hear about the flakey LOR. it can be frustrating. Same thing happened to me. After my one recommender was MIA for two weeks after submission, i emailed director of graduate program told them everything! the director was super chilled and said i still had time to send through my LOR via email to her or through the portal. At that time I emailed my back up recommender to send an email, and she did on that evening, and so did my original recommender - so i have four for that application.
So I'd recommend you email the school and let them know what has happened.