I think you can rarely skip entire years as a med student even after taking an SMP. It might be possible to waive a course if you took it at their school during your SMP, but if it is a school outside the SMP, then they can say that it might not be up to their standards, and you'd have to take everything again. Each school has their own standards.
If you do end up waiving a course they may make you be a lab TA or something so you remain in that year's class, but still take the class in some form or another. My friend already had general pathology so didn't have to take that, but they required him to TA the lab for his class.
SMP's are great programs, but like all post-bacc/grad programs, they aren't an all encompassing "warp zone" into med school. So yea for the most part, you should probably expect to retake courses, which isn't such a bad thing since you should do well in them anyway.