Its possible for the Lucas10AS to loose sync with the fob, I had this happen on the D1 after replacing a flat fob battery.  Obviously not the issue in your case.
You're correct about the fob and the ignition as there is nothing to power the fob but the battery so it would immobilise the vehicle.
I don't suppose you tried the EKA did you?  Would have been interesting to see if this did anything.
Also the alarm light  that flashes at the bottom of the speedo should pulse differently if either the fob or the vehicle battery is showing signs of low voltage.
Might pay to give drivesafe a PM about the SC40 and the second battery.  If the second battery is on the way out... well remember what happened to mine last July.
Sorry that none of this sounds really helpful.
				
			 
			
		 
			
				
			
			
				MY15 Discovery 4 SE SDV6
Past: 97 D1 Tdi, 03 D2a Td5, 08 Kimberley Kamper, 08 Defender 110 TDCi, 99 Defender 110 300Tdi[/SIZE]
			
			
		 
	
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