There is nothing magic about the Traxide system. All it does is disconnect the starter battery from the aux battery when the voltage drops enough. The rear Anderson plug is just a direct connection to the aux battery. If you apply a voltage to the Anderson plug it just applies that voltage minus losses in the wiring to anything connected to that circuit. It will also apply voltage to the starter battery if they are connected at the time.
I'm not sure what you think is happening but that is all it is. The Traxide system won't affect anything that you plug into it and can't damage anything by itself. There is probably either a problem with the way you have plugged the Thumper into the system or the CTEK is faulty. Failing that, there could be a problem with dissimilar battery types being connected together. The starter battery is a calcium battery which can be charged at a higher voltage than AGM or conventional batteries but I don't know what your other two batteries are. Perhaps the Thumper didn't like the voltage that the car was providing to charge the starter battery and that was what cooked it. The CTEK wouldn't charge because the battery was already cooked.
The Optima AGM battery that is usually used as the aux battery in D4's is more robust then most AGM batteries and doesn't mind high charge rates and voltages and is perfectly suited to the D4. It is possible that the thumper is not so suitable but you haven't provided any info on how it is connected to the system or what type of battery it has that I can see. Is it connected via the 12V plugs in the rear that are part of the Traxide kit?
What do you mean by a cooked battery? Is it boiling, not holding charge, low voltage or what?
				
			 
			
		 
			
				
			
			
				Bob
2010 D4 3.0TDV6 SE, ediff, LLAMS, 5 x GOE wheels, LT285/60R18 BFG K02's, GOE Compressor Guard, LR Tank, Mitch Hitch, ECB Bull Bar, Kaymar Rear Bar, Traxide, Safari Snorkel.
2019 Discovery 5 SD6 SE, 20 inch wheels, 275/55R20 Nitto Grappler G2 tyres
			
			
		 
	
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