Hi all.
Just an update. I didn't get anyone reply with any answers for this issues so I assume that nobody had fixed it without main dealer help.
I did have my car booked into a dealer to have the central convenience module flashed and keys recoded for the 23rd but I have managed to fix it myself.
As I said earlier, I scanned my car with vcds and didn't get any relevant errors. The only error I got was a reoccurring error stating that the car had gone into power management (essentially the battery is knackered).
This must have been what caused the keys to lose their programming to start with. The confusing thing is that with the B8 A4 and A5, the remote is automatically reprogrammed everytime the key is placed into the dash slot and the car turned on. This was not happening with mine.
I was out of options.
I then thought that maybe the power management knocked out the central convenience module (to save power for starting) and this had caused the unit to restart but not quite started back up correctly. Remember, vcds was showing no errors for the ccm.
I tried looking on vcds for an option to completely restart the module but no job.
I decided to find the ccm (which I located inside the boot, on the right hand side and is a fairly large unit with about 6 cable connectors going into it.
I unplugged all of the connectors and left the car for 2 hours. MAKE SURE YOU DONT SHUT THE BOOT, YOU WILL GET LOCKED OUT, because the ccm controls all remote functions and all lock functions including the boot switch on the drivers door.
I got back to the car, plugged all of the connectors back in, put my key in the dash, started the car, pulled the key out and hey presto, key fob works again!!
So before you give up and take your car to the stealers to be reprogrammed, simply unplug the module for a couple of hours and it will be reset and should work again!