What is the problem you have?
DirectX have a limit on 32 buttons per device, so I assume your device shows up as two separate devices. This should not be any problem for Elite to use both of these devices at the same time and assign functions to each of the buttons present on these devices. This is not a limit that FDev or any other game developer really can bypass, if they are using DirectX, then the limit is 32 buttons per device, until Microsoft decides to update the definition to support more than 32 buttons per device. If the device present itself as a keyboard, then we do not have the limit of 32 buttons.
I have a multi function panel with 50 buttons. I also have my throttle, joystick and pedals all matched up into 3 virtual devices by my controller software.
So to Elite, I have
CH Device 1 - 32 buttons
CH Device 2 - 32 buttons
CH Device 3 - 26 buttons
Elite has no problem finding these or use any of these 90 buttons I have available.
As long as your device shows up as DirectX devices, it should not matter if it is spread over 2 or more devices. Elite however is a bit dumb when it comes down to showing which device a button belongs too, so you most likely have two devices,. we call the A and B
A: 32 buttons
B: 16 buttons
For example, you assign A:button 1 to cargo hatch,
then you assign B:button 1 to landing gear
Now Elite will show that "button 1" is bound to both cargo hatch AND landing gear. Which might look very odd, but that is just how Elite shows it. And if you actually try to map A:button 1 to another function, it should alert you that it is already in use and if you go forward with the remap, the binding to cargo hatch will be cleared.
So what is the issue you are facing? It could also be that the driver software that comes with your device needs to be setup to present the throttle as DirectX devices, or that if it is loaded, does not by default present it as DirectX devices. I have the option to present any of my buttons as normal keys, like "j", "1", etc, instead of DirectX buttons.