Removing modules from schematic

I am trying to remove some modules from Rpi compute module 4 IO.

Using nightly version of KiCAD for this project. Even after removing the modules, and after importing the changes to the PCB, the connections remains same.

Please help

How do you do this:

Normally it’s done with Eeschema / Tools / Update PCB from Schematic [F8]

And what do you mean with:

KiCad does by default not delete footprints from the PCB during this update. There is a checkbox with [ ] Delete footprints with no symbols in the Update PCB from Schematic dialog.

Updating the netlist does not change anything on tracks laid in copper on the PCB.

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