Question: How would it affect my junior student who is currently taking IB courses if he only took AP classes his senior year.
If your rising-senior son is in an International Baccalaureate Diploma program and then drops out at the end of his junior year, it will raise a flag or two for admission committees but isn't a deal-breaker. He should, however, provide an explanation of this choice, using either the “Additional Information" section of his applications or a separate letter.
Obviously, there are some explanations that will play better in admissions offices than others. For instance, if your son is opting for Advanced Placement in order to avoid the most rigorous IB classes, favoring instead some of the AP alternatives that admission folks might dub the “fluffy" ones (e.g., AP Psych, AP Econ, AP Environmental Science) then this revised schedule could hurt his chances at the colleges that are the most hyper-competitive. Even if his explanatory letter points out that these are the subjects that interest him the most and that intersect with his career goals, admission officials may be apt to publicly nod in agreement while privately inching your son's application toward the Reject pile. 🙁 However, at colleges where admission decisions are not so hairsplitting, a change like this one should have little or no negative impact.
But if your son's AP load will be as challenging as his IB classes would have been and includes heavy-hitters like AP Calculus, AP Physics, AP Chem, AP History, etc., the admission folks won't be so wary of the change, but they will still want to know why it happened. Perhaps there are logistical reasons (e.g., IB classes conflict with band, yearbook, or some other endeavor that your son is passionate about) or maybe the IB program at your son's high school is not well organized and/or the best teachers seem to be assigned to AP. These are all valid reasons for the new plan that should be reported to the colleges.
The bottom line is that your son needs to pursue the program that feels right to him, regardless of how it will be viewed in admission offices. But you also should realize that admission officials will be curious about why your son made the 11th-hour switch. You don't want them to attribute it to phantom problems such as a disagreement with a teacher or program director; frustration with the work load; even anxiety or depression, that don't actually exist at all. So make sure that your son provides his rationale for the new direction … and, ideally, it's one that emphasizes his love of learning rather than his love of wangling a little more free time. 😉