Does anyone know what modules need to be changed to completely shut off a factory Bluetooth unit so as far as the cars concerned it doesn't have one!?

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You'll need VCDS to achieve this. If you're familiar with it, or have it yourself, do the following;

 

Goto CAN Gateway – Controller 19

Re-coding should be carried out using the Long Coding Helper. Select Byte 3 and put a tick in Bit 7 to enable Controller 77 Telephone. Write the Long Code back to the car.

 

You can also enable/disable via the Gateway Installation list, which achieves the same coding change as the steps above.