are you talking about the primary app, or the secondary app? I'm assuming you're talking about the secondary. I applied last year, and from what I remembered, it's a paper app right? If you use a letter service at your school (or committee letter), wouldn't it take some time for them to pull out your letter and mail it? so I say you're probably fine. Even if you're sending the rec. directly (by yourself), a couple days apart will probably still be OK. I assume that med school will keep your letter for a little bit since they already have your file in their records (or else they wouldn't have sent you a secondary).
but if you want to be sure, just call them and ask. they're nice people.