Anthony,
It looks like you're in the gray area of 4150.2 without any specific instructions
The VC Sheet under VC 9 states "That FHA will accept a maximum of 3 layers of existing roofing" and that's what I'd personally use to get me out of your problem.
What you have is a basic safety issue. Most roof structures can safely support 3 layers of roofing, some only two. After that, there's a danger of excessive dead load on the roof. More than 3 layers on the roof makes me wonder if the owner had it professionally installed and if a building permit was issued for the work. I don't think many towns would allow more than 3 layers due to the safety issue. So that's another red flag-possibly no permit was issued so as to avoid the town's building/safety code.
Report what you have seen/your concerns under VC 11G as to the "safety" of the existing roof and let the DE underwriter deal with it from there.
If the DEU is happy with more than 3 layers and wants to have an engineer certify that the existing roof structure/framing can support the additional weight, s/he can do so.
Just report what you have seen and throw it on the DEU and the experts.
Ben