how to delete a part of the design using ECOs

Hi all, I have a circuit design containing 2 parts, the first part can run on it own, while the second part gets some input from the first part and gives some outputs.

Is there any way that after compiling, I can use ECOs mode to delete the second part so that I can have two netlists, one with the second part and one without the second part?

Because I want to use side-channel to evaluate what the difference caused by the second part only.

I tried incremental design technique but it didn't give the result I expected. The routing and placement of the first part in 2 designs (one with the second part, one without the second part) are still somewhat slightly different.

I want to keep it exactly the same.

Thank you so much for reading.

:)