Hmmm, I would check the "Load Sense" wire from the back of the alternator to the batteries. I don't know as there is a diode in line with this wire, but if my memory serves this is a direct connection. On the LN alternators, there is a ground wire which is not needed if you change to a Delco model. I have not experienced this issue more than once when we did have dead starting batteries after leaving the coach unplugged for a month. Engaging the boost switch got me started, and since then no issues.
Rained from about midnight to dawn in Las Vegas, NV.
Monty & Janet - 2007 Alpine APEX 40 MDTS
S/N - 75715 - Retired - Master Certified RV Tech