With PackageKit-0.9.4-3.fc21, I see both /var/cache/PackageKit/hif and /var/cache/PackageKit/hawkey being used, with almost the same contents, which seems strange.
We moved the upstream bugtracker to GitHub a long time ago. If this issue still affects you please re-create the issue here: https://github.com/hughsie/PackageKit/issues
Sorry for the impersonal message, and fingers crossed your issue no longer happens. Thanks.