The RPUno controls power from the battery to its VIN pin with digital IO2. On the RPUpi shield that power is provided to an SMPS that provides 5V at up to 1A to the Pi Zero header. Wait... don't just pull the plug, the correct way is to halt the Pi Zero and then wait for it to stop. The time it takes to halt depends on the running applications. The best handshake I have figured out is to wait for thirty seconds and then watch that the load current from the RPUno battery has stabilized as demonstrated with this Power Management firmware.
The RPUpi has a shutdown button that pulls down BCM6 (header pin 31) on the Pi Zero. BCM6 is used by a Python Shutdown script to halt the computer. For testing, I've loaded the bus manager with the Remote* firmware that places a weak pull up on its PB0 (ICP1) pin which is also tied to that BCM6 pin through a 1.8k resistor. As a result, both a manual or bus manager initiated halt can occur. The RPUno must check for a manual halt by reading the shutdown_detected flag from the bus manager as demonstrated with the Power Management firmware.
The RPUno also controls power to the FT/Pulse sensor current sources with digital IO9 and is also demonstrated with the Power Management firmware.