It sounds like you have a good amount of time invested in the project already. From your story so far, you seem to have a good grasp on how the two units interact during operation. From your description, it sounds as if the panel issues commands and the main module either acknowledges the command or replies with an error message. There may be other communication going on that may seemingly have no effect on operation.
The tool you seek here is a logic analyzer. There are literally a jillion of these things on the market to suit many needs. In this case, the hrv controller probably runs in the single digit MHz range, and comms much slower. A cheap, USB-based probe will more than do the job here. Just search for "usb logic analyzer" or "pc logic oscilloscope" and the like. If the unit does indeed chat back and forth, it probably speaks i2c, spi, or some other common language. There are open-source interpreter programs on the web that can help you figure out the details. As with all software, the paid versions are usually better once you learn the process.
If you decide to go the other way, the manual does a pretty good job at spelling out most of the details behind the scenes. The unit seems to use a 10k nyc thermistor for the defrost sensor, so it wouldn't be super difficult to interface with. The relay and motor drivers could be found and tied into. Then you would have to write a firmware of your own.
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