I changed to small screw terminals, knowing this would occur. But I cannot find me a tool which can do this via removal for me.
I think that this tool could benefit from extra lines like:
Delete Vias if they have a wrong net
Delete Vias if they are merged in a pad
or something betters.
No, you did not run the tool. To run the tool, you have to click on the Build Changes button first. Only after that KiCad shows a list of the changes to be made and the text on that button changes to Update PCB.
There are apparently also some subtle changes in how KiCad V8.0.5 handles via’s with fixed net names, so also update to the latest stable version before further testing.