Currently Meson fails to reconfigure if it is upgraded. This is not good.
Dylan is working on this with the upstream Meson project.
This should be fixed as of 0.49.0; when 0.49.1 or 0.50 comes out meson should automatically reconfigure as soon as it's invoked by ninja.
meson issue: https://github.com/mesonbuild/meson/issues/4635