Oh dear, just got off the phone from EMEA Techincal Support, Apparently I am not allowed to upgrade the drives and because I have my 2 year warranty is null and void. Actually it was less monochrome than that, still not entirely sure whether I can remove a drive or not without voiding. One is "ok" at my own risk, but opening the box exposes me to a risk of electrocution. I think what they didn't like was the tftp boot that apperently is definately outside the warrantly as far as they were concerned. Everything I did was documented in the KB or on their website so it rubs a bit.
I looked at all the warrenty info on the Buffalo website and it is pretty general so they could void you for most things in theory. I haven't found anything that tells me that I am not allowed to remove a drive on the LS Pro Duo specifically, and given the easy access front bezel and the raid feature you would expect to be able to swap out a drive - but maybe not.
Ironically it was the firmware update that appears to have messed the unit up. I imagine that some bootloader that sits in the units flash memory didn't get reflashed right - is there anyway back from here, can I flash the memory by connecting to points on the PCB. I am sure it is something Buffalo could do but it looks like I am on my own as far as they are concerned, Ideas anyone?