Android Auto stopped working in Nikki's 2018 Honda Civic tonight out of nowhere. For anyone who has this issue, for us a reset on her audio system was the fix. Going to Settings, System and doing a Factory Reset. After that, when we plugged a USB cable into the Android Auto-compatible port and connected her phone it successfully started setting it up again.
It actually didn't entirely set it up properly until we also manually paired HandsFreeLink, by disconnecting the cable first, then pairing it through the car's Bluetooth menu.