made some progress today...
I was able to image the first 3 partitions off the original HDD and copy them over to a new HDD (although its only 160GB for testing). I tried to partition the remaining space into XFS using a GParted live cd but it threw an error so I had to just leave it as unallocated space.
Put the drive in the nas and it loaded up. I used the latest firmware 1.12 from Buffalo in debug mode to push a firmware update (with do not check version and force update only ticked from the right panel and all the left panel selected). I did try to use the rebuild partition table option and could see it sending the firmware files, format, send firmware, write firmware and then it tried to reboot and gave me the 6 flashes - HDD not recognised. Anyway the firmware update worked. then I used erase disk from the web interface to clear out the shares it still thinks should be there from the last disk.
So now I am left with a fresh install BUT its giving me 4 flashes. I can access the web interface and at the moment the shares as well but will keep playing with it for a while to make sure.
The manual says 4 flashes is RAID error but it only has one disk so not sure what that means.
Anyone able to shed some light on it?