The online systems make it quite obvious that one is either not submitted or requested but not uploaded (yet). I think the way to do it is simply remove that person from the list and add another.

The problem is it only gives me the option to exclude a recommender. The issue is that my recommender is not receiving the notification email to submit her letter. I was going to create a new recommender with her other email, since its a little too late to contact admissions since the deadline is Monday and then exclude her other listing.

They usually allow extra time to resolve technical issues or delays. Deadline is deadline but there is some time given after because not every recommender turns things in on time. These are things out of your control.

Try contacting the support systems for whatever service is used. If it's technical, they might be able to sort it out internally. Assuming you followed the junk/spam mail check, the only other thing I can think of is to give admissions a heads-up come Monday and do whatever seems to work to fulfill the required number of recommendations.