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Oh, forget and just close this. I was able to fix it myself with the following steps:

  1. I ran rpm-ostree status -v as root in the console, then I was able to see that "libvirt libvirt-client libvirt-nss" and some others were in the "InactiveRequests" state (i.e. those were both layered packages and base-installed packages);
  2. Then I just ran rpm-ostree uninstall libvirt libvirt-client ..., and after this I was able to rebase successfully.

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Answer selected by dacampsss
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