I have two SPI encoders that are both throwing a COM_FAIL, the encoders and cables both work on a second ODrive. I have updated the firmware and redone the configuration to match the working ODrive.

That’s strange. 3.6 or Pro?

It’s a 24v v3.6. It shows at startup, and won’t clear when I call clearerrors().

Tbh it’s more strange that it works on another ODrive lol. It’s common to have to add tri-state buffers and such because of the way the SPI encoders work. Check to see if it’s outputting an encoder error in the “error flag” spot.