I too am having one heck of a time. I bought an xbox one 500 GB from ebay that had one of the E200 error codes. I've been trying for over a week to get this thing working, following all of the wiki's/posts out on the internet. I am successfully able to format/repartition the drive using Ubuntu and the scripts/tools. the "drives" application reports a SMART status of OK. However, anytime I have either put the contents of the OSUDT2 files on either the newly formatted drive in the A and B folders per the instructions, or a flash drive, I receive an error. My latest attempt was to simply format/partition/unmount the HDD in Ubuntu and then install the blank but newly formatted/partitioned drive in the xbox and install the OSUDT2 file from MSFT via a USB drive. Yes I ran that script that says "are you sure you want to make this an xbox HDD?" The console was able to install the update and reboot, but during the "applying update" phase it reached 66% then threw the "something went wrong" page and error E200 again. I'm going to try using the factory reset via USB on it next.
Do these consoles have the ability to format/partition a bare drive on there own? I would think the easiest approach from MSFT, would be if a drive failed, simply take it apart, put in a new drive of the same size, reassemble, then run the OSUDT file from USB to re-install the OS - but alas, it doesn't appear that works.