Hey Joe,
good question. There exist two limit sensor pins (9, 10) for the second Y motor and I assume you connected a sensor there.
I haven’t tested it yet (I don’t plan to use this controller but have one here (running and connected to the network) in the lab so I can test things (when I’m there).
Do you have a normally-close setup? Which produces an error if you try to home but the sensor isn’t there? If so, if you disconnect the slave sensor and try to home Y, what happens?