I actually got a reply from Vera support and they offered to call me to help out. After 45 minutes (which was mostly consisting of waiting on Vera the issue was resolved).
I hope that none of you would ever have to deal with this, but in case you do, these are the steps to follow:
(The document is from Vera support, I've just made a few minor enhancements. I also used the Putty as telnet client)
How To restore Vera 3
- Connect your computer directly into the LAN1 port on the Vera3 unit
- Plug the power adapter in Vera and when the power led starts blinking red (amber), press and release the reset button.
This is the most important step because it puts the unit into flashing mode. If this is successful you will see the the power light blink red/green very fast. (If you press the Reset button while plugging in the power cord it won't work)
- Put a static IP on your computer (192.168.1.2) and the gateway 192.168.1.1
- Run Putty and select connection type to Telnet. Make sure that the port is set to 22 and type 192.168.1.1 as host address. When you are connected type (or rather paste) the commands below. (The third command will reboot Vera and in my case I never saw a response on the Putty terminal - it acted like the Vera hung)
flash_eraseall -j /dev/mtd7
echo b > /proc/sysrq-trigger
Now the Vera unit should reboot and you should see it booting up. It might take a couple of
seconds, first the LED should be solid red, then green, red and after that it should boot up
6. Change your IP address back on automatically or 192.168.81.2 and gateway 192.168.81.1
7. Check that the Dashboard loads (i.e open up a web browser) on 192.168.81.1 after all the LEDs are on and solid green.
After this I went to the Vera UI and Settings | Backup and chose an relatively old backup (checked the Restore Z-wave network checkbox) and 20 minutes later my Vera was back to it old self again.
Tried again to install DataMine2 and this time it seems to work without breaking Vera.