After waiting to see if the next tuesday updates would fix my issue of undeleteble 46MB and KB4058258 not insallable, I also went for this in-place upgrade and all went fine...

I have the exact same issue (same 46 MB "undeletable" from WU) together with kb4058258 that fails with error 0x80070bc2 (after reboot).
I tried almost whatever I could imagine except update from...