I can’t really help you with your current boot problem, but the way I protect mine from power loss is I’ve got mine powered by one of these: PowerBoost 1000 Charger - Rechargeable 5V Lipo USB Boost @ 1A [1000C] : ID 2465 : $19.95 : Adafruit Industries, Unique & fun DIY electronics and kits combined with a 1 cell 10Ah LiPo battery (extracted from a cheap phone backup power pack).
There’s also these: LiFePO4wered/Pi+ | Crowd Supply for a more compact option that can automatically do a clean shutdown, but you’d need to check the pins used by the EmonBase don’t conflict (and get the one with the stackable headers).