Honestly, time will tell. They will have a lot of updates for us come the AOA Annual Meeting in late June. People on this forum may hear speculation from program directors or from leaders within AOA who are affiliated with their school, but it's tough to get a reliable estimate as there are so many variables. Someone who sits on these actual RRCs might know best, but I personally don't have connections to these people.
Early in the single accreditation system planning, the AOA, particularly Boyd Buser, DO, has told us students through webinars and public speaking events that they anticipate that most/majority of programs will successfully make the transition; unfortunately, I don't have any sources to provide you on that as those webinars aren't available any longer as far as I can tell. The ACGME of course doesn't like closing programs so it is in the ACGME's interests to help AOA and borderline programs to meet standards with substantial compliance during the transition.
Keep in mind, that to gain initial and continuing accreditation, programs need only to be "in
substantial compliance with the applicable Program Requirements and/or the Institutional Requirements."
http://www.acgme.org/acgmeweb/Portals/0/PDFs/Nasca-Community/FAQs.pdf Substantial compliance means they don't have to meet all requirements at 100%. Some requirements are much more important than others (core req vs detail requirement) and is a bit of a subjective judgment. They look at the whole package and make a decision. Again, I think someone who actually actively sits on a RRC would be the best resource on answering your question reliably.
I can tell you of some specific programs saying they intend not to apply based on their AOA Opportunities entries:
Family Medicine/Emergency Med at McLaren Oakland in Pontiac, MI
Otolaryngology in Wyoming, MI
Ophthalmology in Wyoming, MI
Dermatology in Cuyahoga Falls, OH
Ophthalmology in Las Vegas, NV
Emergency Medicine in Portsmouth, OH
Family Medicine in Portsmouth, OH
Interesting link pointing out the most common reasons of citation for withheld accreditation:
http://www.osteopathic.org/inside-aoa/single-gme-accreditation-system/Pages/default.aspx