As the parent of a now-senior son who transferred for academic reasons in the middle of 10th grade -- I would like to pass along a few thoughts.
First, if she is in a crisis mode, then absolutely, find a way to alleviate her stress and difficulties, without worrying for a moment about impact on college apps. Her mental, and physical, health is paramount.
Then, I would suggest considering what she will be getting out of coursework over the next two years in either IB or AP program and whether it suits her interests and learning styles. Does she have particular academic interests that are met with either curriculum? For instance, at my son's IB program, it is still a newer magnet and so there is not as much depth in IB Math and Sciences as the best Math/Science students might want, so they tend to take AP Math and Sciences or more advanced work at local community college etc. and may, for that reason, not be full diploma students. This hasn't mattered to him as he is an English/History type kid, but it could be a consideration for someone who wants AP Bio, Calc BC etc under their belt before college.
Can you or your daughter talk to some current 11th and 12th graders at the local school to find out about the AP courses? How good are the teachers, how well-prepared for the exams are the students? Do the students like those classes? My son, which is just my experience, had some AP classes because of scheduling issues, and preferred the seminar-based IB courses. AP felt relentless in a way that he did not feel in IB. Again, that is my son, not your child, so I would encourage you to ask around and get a better feel for student experience at the local school.
If you are thinking about college admissions, you might consider each schools' track record of placement at the type of schools your daughter might be considering. Separate from the question of any local ranking of high schools, sometimes particular colleges just are more familiar with the students and the level of qualifications from different schools, based on how many apps they have received in the past, students they have admitted etc. For us, so much changed over four years in terms of our son's growth, the insanity of admissions etc -- we thought we knew what we might be looking at when he was in the early high school years, but that evolved dramatically. If you spend much time on these boards, you know the spring has been littered with valedictorian, award-winning, varsity sports, great everything students declined at top 20 schools so that they are now deciding among some great merit awards at the next level schools. That great resume gets a student in the door, but 9/10 will be declined, even though all of them are capable of success at the school.
Good luck to you and your daughter, it sounds like either school will be a good place for her.