@kbabilinski well, this is REALLY weird, but I have got it to work again. What I did was install the ML3 hub on a different device - my lowly Surface Go 3, download 1.8.0 on it, connected the ML2, and run flashall_amd -e again.
And it quickly installed everything. Okay, so now I have lost all my settings, but I have a functional device again. I am starting to think there is something that has changed on my main desktop computer that does not work well with Magic Leap. Anyway, going to install 1.9.0 again. Using the Surface Go 3. Fool me once 
Update: 1.9.0 flash was successful as well. 