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It is a bit incomplete as a test case as you didn't provide any script to run in yosys. I made one up and I see the general trend you describe.

I also see a lot of constants being passed through the hierarchy in your netlist. Those case can't be optimized when running hierarchical synthesis. In the flat case they can. I suspect you have effectively disabled almost all the logic in your design this way and so yosys optimizes it away. Its a bit hard to tell in a large generated .v file - is that your intent?

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