Configuring stereo input channels or mixbusses is done on show level. You cannot change that configuration by loading a scene. Furthermore changinge the mono/stereo configuration will cause a short audio dropout since the FPGA must be reconfigured.
The newest firmware version ( afair since V1.4) you can use Ganging of channels to link certain parameters of two or more channels, which is suitable to create stereo channels in an other way which can be stored on scene basis. But you can only create eight of such channel groups.
The other possibility is to define enough stereo channels in the very beginning. Then assign the desired input sockets for the stereo channel for the first scene. Let‘s say you define the channels 37/38 as one stereo channel. You want to use it for your e-piano which is connected to input 11 and 12. assign those inputs to the stereo channel and place the fader of that channel as you like on your favorite layer, lets say fader 11 on Layer 1. Now it seams that on your first layer the piano is where it should be (fader 11, which is corresponding to the first used input socket) and everything is fine. You can store that configuration to scene A.
Now, when configuring scene B you want to use that stereo channel for a Synth on input sockets 15-16. change the input assignment, place the stereo channel somewhere elso on the layer and, voilá, you have a differt usage for the same channel.