I'd want to know whether the third recommendation letter is important. In other words, whether the order of recommendation letters is important in applied maths or all the letters of recommendation are equally important.
If somebody asks for your letters of reference, they will ask for all of them. So the order in which they’re listed doesn’t really matter—particularly since they might arrive out of order anyway.
Since you're in applied math, you're likely using MathJobs. It's true that the order you list your recommenders is the order they'll show up on the committee's side. But that order doesn't really matter. The one exception is if you have e.g. a fourth letter that only addresses your teaching (not your research); in that case I would list that letter last.