If you're having repeated 12v battery issues, I would make absolutely sure that you don't have problems related to either the modem being stuck on or water intrusion in connectors. I bought a salvaged 2014 Energi for a great deal b/c it would die every time the HVB was charged. The gentleman that rebuilt the body thought they were getting the car at a steal but couldn't figure out the wiring issues. Being salvaged, all warranties are void. Water had gotten inside and corroded the connectors for the ICE water pump and vacuum pump (both electric of course). These both draw quite a bit of current and would run continuously whenever the vehicle was running or charging. This would result in frequent dead 12v batteries and no-starts. I was able to get the TSB from Ford for the water intrusion issue. A helpful service rep also texted me pictures from the service manual that lists the affected connectors. Sure enough, three of the listed connectors had bad corrosion. After a new water pump and pigtail kit, and some new DIY connectors my battery drain issues are gone. I also neutered my modem by pulling out the SIM card. I don't have access to MFM but I can still edit my GO TIMES and value charging manually from inside the car and they work flawlessly.
There appear to be lots of things that can cause 12v battery issues on these rigs, these just happened to be mine. Ford dealerships seem to be mostly ignorant of PHEV's and, at least in my neck of the woods, see very few of them. In the end, after LOTS of research and time under the car, I got a steal at $8,200 for a car with 24,000 miles on it. I'm sure we can figure out yours.
Attached is 2 service manual pics that detail locations of the affected connectors.
TSB 15-0089 ENERGI – DISCHARGED 12 VOLT BATTERY