Rpmdb missing ~1000 package records after F43→F44 upgrade; rpm -qf reports core files as unowned

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After upgrading from Fedora 43 to 44 (KDE spin, dnf system-upgrade, 2026-08-29), rpm reports that most files on my system aren’t owned by any package, and many core packages aren’t in the database at all — even though the files are present and working normally.

$ rpm -qf /usr/bin/zsh
file /usr/bin/zsh is not owned by any package
$ rpm -q man-db
package man-db is not installed
$ rpm -qf /usr/bin/tmux
file /usr/bin/tmux is not owned by any package

zsh is my running shell and tmux works, so the files are clearly there and functional.

What I’ve ruled out:

  • Not a dnf/rpm mismatch. rpm -qa | wc -l → 1481, dnf list --installed | wc -l → 1477. They agree.
  • Not a wrong dbpath. rpm --eval %_dbpath → /usr/lib/sysimage/rpm. No ~/.rpmmacros. /var/lib/rpm is a correct symlink to ../../usr/lib/sysimage/rpm, and rpmdb.sqlite is 95MB.
  • Not a permissions issue. Same results as root and as my user.
  • Not a container or image-based install. Plain F44 KDE, rpm-ostree not present.
  • Not a broken rpm binary. Packages installed after the upgrade register correctly — I reinstalled ghostty today and rpm -qf /usr/bin/ghostty resolves it immediately.
  • dnf distro-sync reports nothing to do.

The part I can’t explain: dnf history info 211 for the system-upgrade transaction shows Status: Ok with both begin and end rpmdb checksums recorded, and the listing covers the full F43→F44 package set — installs, upgrades, replacements, 20 groups, and the KDE environment. So the transaction claims it committed. But 1481 records seems low for a KDE spin; I’d expect well over 2000.

So the database appears internally consistent and the upgrade reports success, yet a large number of package records seem to be absent.

Questions:

  1. Is there a way to determine what actually happened here?
  2. Can the missing records be rebuilt from the dnf transaction history, or is reinstalling the package set the only route?

I’ve held off on rpm --rebuilddb since the primary table itself looks incomplete rather than just the indexes — I don’t want to make things worse.

System: Fedora 44 KDE, kernel 7.1.10-200.fc44, rpm 6.0.2. Upgraded from F43 on 2026-08-29.

Abbreviated dnf history info 211 output below.

   1 │ === dnf history info 211 ===
   2 │ Transaction ID : 211
   3 │ Begin time     : 2026-08-29 14:19:45
   4 │ Begin rpmdb    : a4d39ac7fd3d3dcfd4de63dae5b88bbbf07b96b949ee7d0da04fe94367a2fd97
   5 │ End time       : 2026-08-29 14:23:52
   6 │ End rpmdb      : 68b3087f64fa8a4714d1149ceaeb9b4c7a8d587c26a7c589198d90f9ccbc2006
   7 │ User           : 0 Super User <root>
   8 │ Status         : Ok
   9 │ Releasever     : 43
  10 │ Description    : dnf system-upgrade download --releasever=44 --disablerepo=fedora-cisco-openh264
  11 │ Comment        :
  12 │ Packages altered:
  13 │   Action    Package                                                        Reason          Repository
  14 │   [... 2400 lines of package list omitted ...]
  15 │ Groups altered:
  16 │   Action  Package                   Reason     Repository
  17 │   Upgrade admin-tools               Dependency fedora
  18 │   Upgrade anaconda-tools            User       fedora
  19 │   Upgrade base-graphical            Dependency fedora
  20 │   Upgrade core                      Dependency fedora
  21 │   Upgrade desktop-accessibility     Dependency fedora
  22 │   Upgrade dial-up                   Dependency fedora
  23 │   Upgrade firefox                   User       fedora
  24 │   Upgrade fonts                     Dependency fedora
  25 │   Upgrade guest-desktop-agents      Dependency fedora
  26 │   Upgrade hardware-support          Dependency fedora
  27 │   Upgrade input-methods             Dependency fedora
  28 │   Upgrade kde-apps                  User       fedora
  29 │   Upgrade kde-desktop               Dependency fedora
  30 │   Upgrade kde-media                 User       fedora
  31 │   Upgrade kde-pim                   User       fedora
  32 │   Upgrade libreoffice               User       fedora
  33 │   Upgrade multimedia                Dependency fedora
  34 │   Upgrade networkmanager-submodules Dependency fedora
  35 │   Upgrade printing                  Dependency fedora
  36 │   Upgrade standard                  Dependency fedora
  37 │ Environments altered:
  38 │   Action  Package                 Reason Repository
  39 │   Upgrade kde-desktop-environment User   fedora
  40 │
  41 │
  42 │ === rpm -qa count ===
  43 │ 1481
  44 │ === dnf installed count ===
  45 │ 1477
  46 │
  47 │ === spot checks ===
  48 │ file /usr/bin/zsh is not owned by any package
  49 │ package man-db is not installed
  50 │ ghostty-1.3.1-4.fc44.x86_64
  51 │
  52 │ === dbpath ===
  53 │ /usr/lib/sysimage/rpm
  54 │ lrwxrwxrwx@ - root  9 Apr  2025 /var/lib/rpm -> ../../usr/lib/sysimage/rpm
  55 │ drwxr-xr-x@ - root 30 Aug 15:13 /usr/lib/sysimage/rpm
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