Consider what you’re asking: textures from hill.egg need to be on both sceneA1_palette and sceneA2_palette. OK. But which image file will the newly palettized hill.egg actually reference? The egg file has to name one texture or the other, it can’t say “use this texture or this one, whichever you happen to have loaded.”
So, you’ll need to have two egg files, hillA1.egg and hillA2.egg. Similarly for chairA1.egg and chairA2.egg, and so on. These can be identical before you run them through egg-palettize, but egg-palettize will modify them differently. Obviously, assign one of them to sceneA1 and the other one to sceneA2.
David