This might not work for everyone, but I had this problem too, and was able to "fix" it.
I saw that the newly created second username folder only had a few files in it, belonging to Zune. Just as an experiment, I did 2 things:
Firstly, I rolled back windows, and then uninstalled Zune, and removed any old Zune file/folder I could get to (a lot of old Zune files are out of reach because Windows won't let you in those folders), and then restarted my computer freshly.
Secondly, I also unplugged my external hard drives, because someone from Windows had this mentioned in a list of actions I could do, and this was a simple thing to try, so that is why I did it.
Then I let Windows download and install the update (which was now called 1909 for some reason, in stead of 1903), and it worked. I had my normal username folder, and no .000 folder.
So I am not sure which was the exact fix. I remember though that it happened before that Windows 10 updates had problems when hard drives were plugged in, so this could very well be the issue again.