I understand your concerns, and you are right, of course; there is the potential for problems. However, in my experience, it is unlikely to be a problem. I have been experiencing this issue for some years, without incident, on numerous devices, which is why I am happy to ignore the scan and fix notification. I sincerely doubt you would cause any significan damage, if any at all. This is what my own experience tells me.
As I said earlier, it is about how different manufacturers implement the FS standard. Clearly, it is not so standard. It would be far more comforting to us all if manufacturers would implement FS standards fully and correctly.
I agree with you, it can be disconcreting. It is a problem, for which there is no immediate solution. FiiO could fix this in FW if they wanted to.
I suppose, the best thing is to do whatever you are most comfortable with. I doubt it will lead to problems either way.
It's annoying, maybe FiiO are reading this.