Oh, I see...

Oh so KiCad 5 relative paths do still work, but you have to specify the base directory to start, it does not assume the current project directory. 

Having updated (and broken and then fixed again) some other projects I am working on I at least know how it should work, and how to break it if I do it in the wrong order...

Just a lot of projects to update, and new documentation needed to support this.