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Your issue is pretty rare, I have done the same steps you did on a VM running Fedora 25 and after update and remove unused packages all works as it should. dnf update; ask for continue confirmation, same as dnf autoremove; and autoremove show you the listo of packages to remove, so you know what was removed and you had to confirm. My guess is you have some issue on your disk. Also dnf work as yum with some improvements so it should not cause this kind of issue.