How to document protocol changes across firmware
You should make the way for people wanting to update the firmware too. For this


people should understand if their developments will work on the new version of firmware. If you just change protocol removing previous version, there's a risk that existing applications will not work, and some people will just dump your device. This point is not about documentation, but about your tech strategy;
I would vote for two documents: joint document of the most recent firmware functionality, and release notes which highlight the changes and additions. The size and complexity of these documents depend on the severity of changes to existing API in new firmware.


Of course documents should clearly state which version they are for, when they are released and why. Both documents should be searchable (e.g. PDF searchable with ^F key combination) so that users can easily find words they have in mind.