What? AUR packages have nothing to do with packages installed via Pip.
This is what we did last year for Python 3.10. I don’t see any reason to include anything different. If users install packages with Pip, then that’s up to them to manage them. Nothing to do with Manjaro updates.
It seems we were missing the --rebuildall
Yay flag, so I think it should be:
yay -S --rebuildall $(pacman -Qoq /usr/lib/python3.9) --answerclean All