I've had similar issues updating as well. When I try via the 'buttons' on the xxx.xxx.xxx.xxx:3000, it deletes Kstars from the machine. When I use the iOS app, it'll say it's updating but doesn't do anything. If I use the desktop icon via VNC, it deletes Kstars. I did finally get an update to work via the Android version of Stellarmate app; I used my laptop with a program called 'Lplayer' which is a android emulator. After it completed and I rebooted it did not show that it was updated, but I ran the manual commands (per the FAQ it's "sudo apt-get update && sudo apt-get -y upgrade") and that finished the update and after a reboot it was full up.