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At least on Fedora 26, I found that pkcon refresh force cleared out PackageKit-cached RPMs that were from currently-enabled repositories and had already been installed elsewhere (e.g. via DNF).

There were a few additional cached RPMs remaining for disabled repos that I'd used in the past (e.g. updates-testing); for these I used pkcon repo-enable repo-name, then pkcon refresh force, then pkcon repo-disable repo-name.