If it's 2 Principled BSDF shaders, you can simply mix the inputs instead of the 2 shaders and have only one shader instead of 2.
For example if you have something like this:
Instead of mixing the 2 Principled BSDF shaders, you should mix only the inputs that differ and use one shader. In this case: the Base Color, Metallic, Specular, Roughness and Normal inputs differ. So you can mix the values for these properties with the same masks:
As you can see the result is the same.
So now you can bake those inputs to textures:
As you can see I connected what went into Base Color straight to Material Output and selected Emit pass in the bake settings so it gets saved to the selected new Image Texture node(named after the image's name "Base_Color.exr"). Here is my new Base Color texture after baking:
You could repeat that for other inputs one by one, or use one of many add-ons(like this one for example) to do many textures automatically.