Is there a proper way to clean up old PackageKit caches without resorting to low level
sudo rm -rf /var/cache/PackageKit/2[3-4] etc.
The man pkcon, and PackageKit does not seem to provide a command to clear the cache.
The best method is to tell PackageKit not to cache that is store packages at all. This can be achieved here
#KeepCache=false (to make it look like: KeepCache=false)
And if you use dnf to update, you tell PackageKit not to download any updates automatically:
gsettings set org.gnome.software download-updates false
Also in Fedora 26 and above,
I found that
pkcon refresh force cleared out PackageKit-cached RPMs that were from currently-enabled repositories and had already been installed elsewhere, that is via DNF !