Fedora 23 -- Can I safely delete files in /var/cache/PackageKit/metadata/updates/packages?

From the discussion in the bug linked in Daniel Bruno's answer .. you can get rid of these files using PackageKit console client pkcon

$ sudo pkcon refresh force -c -1

It takes some time but is provided by PackageKit itself. (and you may set a cron job for it)

from the man page of pkcon(1)

   refresh [force]
       Refresh the cached information about available updates.

and

   -c, --cache-age AGE
       Set the maximum acceptable age for cached metadata, in seconds. Use -1 for 'never'.

So this tells PackageKit to delete cached information (refresh cached information with maximum acceptable age of : never)

References :

• https://bugs.freedesktop.org/show_bug.cgi?id=80053#c6
• https://bugzilla.redhat.com/show_bug.cgi?id=1306992#c10

PackageKit is used by GNOME. If you use Yum or DNF on the CLI then don't need these. You can remove the .rpm files in /var/cache/PackageKit/metadata/updates/packages and set PackageKit to not store them any longer.

There is a setting in the file /etc/PackageKit/PackageKit.conf

# Keep the packages after they have been downloaded
#KeepCache=false

As root, remove the hash mark on this configuration option and the packages will not be saved.

Yes, you can safely remove these packages. These packages are only used as cache by Packagekit.

Ref: https://bugs.freedesktop.org/show_bug.cgi?id=80053