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The extender may cut off the lens from the electronic contacts on the camera body. Those have to 'get through' their signals to the corresponding contacts on the lens assembly, in order for Auto Focus (or any other automatic function involving the lens) to work.
I presume that that 100-400 tele lens works fine without the extender in place. Correct me if I'm wrong, and I will amend my answer as needed.
OK, then it must be because the extender cuts off the connection between camera body lens-mount contacts, and the corresponding contacts on the lens assembly.
You can still use the lens in Manual mode.
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