Had the same thing. I just formatted the USB drive to FAT32 and downloaded the new software on the USB Drive. You have to plug the USB Drive into the left USB port or else it won't work. When you start the console you have to hold the start button until it beeps two times. And then click System update with USB Drive. If that doesn't help your HDD is probably bad. Try to change the HDD to another HDD or SSD (if you change it to SSD it will be better) and try the steps that I wrote again. I hope it will help. As I wrote in the beginning I had the same problem with my PS4 Pro and it did help but I didn't change the HDD.
I think it's s overheating try to put the Xbox somewhere else or if that doesn't help try to clean it yourself or bring it to some kind of service like ifixandrepair.
