I think what you're looking for is to only clear the depth buffer, and not the color buffer. That would allow you to render your second scene without losing the rendering of the first.
It seems to me like the depthbuffer is not cleared wvenw hen set to, because objects that are relative to the frustrum nearer than others in the nearpass are, are not overdrawn.
neardistance.setClearEnabled(true);
neardistance.setClearColor(false); //only keep the color results rest is unimportant for the next renderpass
neardistance.setClearDepth(true);
neardistance.setClearStencil(true);
viewPort.setClearEnabled(true); //clear at beginning of the rendering
cam.setFrustumPerspective(45f, 4f/3f, 1000, 10000000);
the seccam is set to same location/rotation before the render and after the update logical&updateGeometricstate
To make sure they really render in the way I want I tried this, but it does not help
Suprisingly the skybox is not renderd in front of the station, this might be because it is far away, to make sure it is only renderd in the farpass, and never in the near one.
Sphere sky = new Sphere(32, 32, 100000f);
The planet is "only" 20000 units from the cam's position