Did you connect the USB HD BEFORE or AFTER this problem developed?
You might have fried the USB Controller Chip when you did that.
Keyboards are NOT desktop computers.
Many are not even up to spec for USB 2.0, much less 3.0, when it comes to delivering current to outboard devices.
Regardless of what you may or may not have done the problem sounds very much to me like a defective USB port on the Yamaha.
It could be a simple cracked solder joint or it could be a fried controller chip.
Either way, with micro, surface mounted components this is way beyond the scope of most DIY repairs.
You'll probably end up having to send it in for service.
I hope you took the extended warranty option when you bought it. It would come in handy right now.
Gary