problems after apt-get update && apt-get upgrade while running rootfs on sata

hi!

I'm running vanilla cli-version of armbian v4-2 on my olimex lime2. However, decided to run it from a sata-attached hdd to improve speed and durability.

the procedure i used is descibed here (and got a lot of help from the creator of the website, thanks!): http://papermint-designs.com/dmo-blog/blog.php?id=3, but i will shortly sum up what i did.

• flashed the sd with armbian cli image 4-2
• let it reboot for it to use the whole card
• created a 10gb partition for rootfs and swap on the sata drive
• changed fstab to mount the rootfs on the sata (removed everything but defaults and noatime because system booted in ro-mode otherwise while running from hdd) :

#/dev/mmcblk0p1    /             ext4        defaults,noatime,nodiratime,data=writeback,commit=600,errors=remount-ro        0       0
/dev/sda1      /      ext4   defaults,noatime   0   1
/dev/sda3      none   swap   defaults           0   0

• copied all files from sd to the sata with this command: 

mkdir /mnt/hdd
mount /dev/sda1 /mnt/hdd
rsync -aAXv --exclude={"/dev/*","/proc/*","/sys/*","/tmp/*","/run/*","/mnt/*","/media/*","/lost+found"} /* /mnt/hdd

• changed /boot/boot.cmd to use /dev/sda1 and /tty0,115200
• updated boot.scr with:

mkimage -C none -A arm -T script -d /boot/boot.cmd /boot/boot.scr

everyting seems to work fine after this and the system boots properly.

so i do:

apt-get update && apt-get upgrade
reboot

the update & upgrade install without errors but after rebooting, i get:

Debian GNU/Linux 8 lime2 ttyS0

lime2 login: root
Password: 
Last login: Thu Jan  1 10:00:26 CET 2015 on ttyS0
Linux lime2 4.2.3-sunxi #2 SMP Sun Oct 11 14:12:18 CEST 2015 armv7l
cat: /sys/devices/virtual/thermal/thermal_zone0/temp: Invalid argument
(standard_in) 1: syntax error

Load: 0.00, 0.01, 0.05 - Board: °C - Drive: 30°C - Memory: 979Mb

and ssh'ing is no longer possible because:

root@lime2:~# ifconfig
lo        Link encap:Local Loopback  
          inet addr:127.0.0.1  Mask:255.0.0.0
          inet6 addr: ::1/128 Scope:Host
          UP LOOPBACK RUNNING  MTU:65536  Metric:1
          RX packets:0 errors:0 dropped:0 overruns:0 frame:0
          TX packets:0 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:0 
          RX bytes:0 (0.0   TX bytes:0 (0.0 

root@lime2:~# ifup eth0
Internet Systems Consortium DHCP Client 4.3.1
Copyright 2004-2014 Internet Systems Consortium.
All rights reserved.
For info, please visit https://www.isc.org/software/dhcp/

Cannot find device "eth0"
Bind socket to interface: No such device

If you think you have received this message due to a bug rather
than a configuration issue please read the section on submitting
bugs on either our web page at www.isc.org or in the README file
before submitting a bug.  These pages explain the proper
process and the information we find helpful for debugging..

exiting.
Failed to bring up eth0.

After i change boot.cmd to boot from sd-card again, reformate sda1, copy everything over with rsync again and change fstab to default, noatime i again have a running system. So did a apt-get update && apt-get upgrade again, but same story :-).

Do you have an idea how i can solve this? Does it has something to do with the changes in my fstab file?

I really would like this system running from hdd, so reverting to sd-card is not really an option for the setup i'm aiming at...

Thanks in advance!