You absolutely must commit the resource.json file. Without it restoration is not safe, and some of the attributes within it define critical metadata.
This is unfortunately noisy, mostly because we constantly attempt to recalculate the 'last modification signature' and reapply it to the file. In 8.3 we no longer do this - if the signature is not valid, we just leave the file alone and assume you know what you're doing.
But fundamentally an Ignition resource is defined by the presence of a resource.json file inside a folder inside a particular folder structure - if you are missing one of those aspects you don't have an Ignition resource anymore.
More info here: