@dc42 It was just a single axis I was trying to home. Sometimes it would home, do its bounce off, and then would appear to loose connection before doing the final slower homing move. When this happened it would appear to run the entire homing routine again for that axis.
I see your point about stepper motor wires, however I think this is different because it seems to be signal integrity problem rather than a broken connection, which isn't something I've ever had issues with on stepper motors. Also, since you can daisy-chain CAN boards, an issue with a single wire could also knock out lots of motors and sensors rather than a single component.
Thank you for raising the event types. I had not spotted that CAN disconnections were included. Looking at it now it says (RRF 3.5.0-beta.4 and later only) though, not RRF 3.4.0. Which one is it? I'm not against upgrading to the beta firmware if that's what it takes, however we are finding that the disconnections often last a lot less than 5s though, so I don't know if it's applicable to this scenario.