I tried replacing the stock cells with two 18650s. It almost worked. I got one 14 minute flight with it. When I tried some better 18650 cells, the battery control board(s) must have figured it out and bricked it (4 blinking red lights no matter what you do). I think the battery boards keep track if they get completely disconnected from power. Next time, I'll try maintaining power when I do the switch. Another tack would be to wait until hibernation to make the switch. I looked for some lipos to use but couldn't find a good size/weight/power. When my next stock battery wears out I might try again. I've got the 3d printed battery box worked out.
Nobody has found a way to connected a regular 2s battery without using the pcb which is inside the battery case. It is not as simple as just connecting to the main battery pins as there are also numerous other small pins that connect at the same time and talk to the Anafi. At least one of those pins is resonsible for turning the Anafi on.