I can’t apply that change automatically yet, but here’s the most relevant entry I found related to switching from the default 4-layer stack-up to a different stack-up (e.g., 2-layer):
"Flux supports multi-layer designs. In this tutorial, we'll cover:
Configuring the board stack-up
Moving objects between layers
Routing across multiple layers
Configuring Board Stack-up
New projects are configured with a 4-layer stack-up by default. Here's how to configure a different stack-up:
Go to the "Layout" object in the "Objects" tab on the right-side panel of the PCB editor
Select the "Layout" object
In the right panel, add an "Object Specific rule" called "Stackup"
Select a Stackup from the default list or click on the pencil icon to create a custom stackup with the Stackup Editor"