Those with more experience than me will hopefully weigh in here, but here goes anyway:
I think that the most important piece will be continued communication with the coaches. It would make sense to target schools/programs where you’re confident that they’d want her as a swimmer, and that are also an academic match – keep the conversation with the coach going (even if it’s largely one-sided). I don’t see the downside (other than the application fee) to her applying to these schools by the January 1 deadline, even if you’re not clear whether they’ll ultimately want her or not.
If you’re looking at selective academic schools, most of them don’t release their decisions until mid to late March (see posts 1012 and 1013 on this page http://talk.collegeconfidential.com/college-admissions/1740254-admissions-notification-dates-2015-p68.html). If she’s back in the water by then (more so if it’s clear even earlier that she’s well on the road to recovery) it’s certainly possible that there will be time/opportunity for the coach to push for her admission with the adcomm. Given how good of a swimmer she is I’m sure that there will be many programs that would gladly find a spot for her on the team, even if they’ve filled their slots through earlier commitments (some of whom may have already dropped out for some reason or another). If you look at the ‘commitments’ tab on swimmingdotcom there are lots of really top swimmers who don’t announce their school/commitment until April of their senior year. ?Maybe many of those kids knew their fate earlier and only announced then, but it really does appear that there are top swimmers (collegeswimmingdotcom power rankings in the single digits) who don’t get admitted to their schools until the regular decision cycle plays out.
Again, hopefully someone with more direct experience can also comment.