Electronic – How to detect the power source when multiple power sources are available

I think you can fix it as follows:

Put a pulldown on sysoff, maybe 100k. Just make sure it is strong enough to overpower the internal 5M pullup. Also keep sysoff connected to your IO expander. It should be configured as an output driven low. But when you want to power down, have the expander drive the output high, which will overpower the 100k pulldown, and turn the system off.

Once the system is off, your rails will all collapse, so the IO expander will be dead, and the 100k pulldown will ensure that sysoff is now low so that startup will be possible the next time charger is attached. You will need to make sure that the IO never goes high during bootup or normal operation. For example, program it to be low before you program it to be an output.

I recommend you verify with FTDI datasheet as well as their support pages (they have a decent knowledge base). I have done a similar design:

You can use any of the CBUS pins of the FT232 to connect to the nBootmode pin of your chip. If the signal is the wrong way, then you can program the FT232 EEPROM to invert it. This means as FT232 powers up, it'll set those pins. You might want to employ a similar thing with nReset of your MCU, that way it'll remain in reset mode until FT232 is up and ready.

You'll likely need to manage separating the power bus using diodes such as a BAT54C or schottky diodes likes this:

Think about what would happen if both power ports are [accidentally] plugged in.

Regarding the PWREN#. It is meant for shutting down power of an external chip during USB suspend. It might be tricky in this case since it is low during USB enum, but it only goes high again during USB suspend which might prevent you from interacting with MCU. You might want use a generic CBUS IO and flick it up or down using the driver or one of the UART lines, etc.

Finally, most FT232 chips can't supply more than 50mA of current. Check that your MCU power requirement is lower.