Probably
Personally my belief is that in the situation that this becomes an issue the government or AMA will step in and attempt to broker a deal, potentially in the worst case with individual schools. I mean my personal belief is that the best option is for all the DO schools and AOA residencies is to merge and be given 5-10 years to buff themselves up. I'm sure most schools will likely either be happily aided by other schools ( ex. MUCOM would be supported by UI or CCOM would be able to receive sponsorship or joint research with RFU or UIC), by the State ( VCOM, CUSOM, ACOM would be supported by primary care and rural medicine provisions and money), or by private benefactors.
Obviously this idea is... idealistic to the point of being silly and unreasonable, but I think it could happen in some way or form.