Opening this bug report in continue to this discussion:

https://discussion.fedoraproject.org/t/after-yesterdays-update-fedora-42-is-stuck-during-shutdown-stage-of-restart/150503/4

In short the dnf5daemon-server can stuck the whole shutdown process in case it's checking for upgrades in the DNF repos.

In my case it was triggered by dnfdragora-updater that was broken and after recent updated started to work properly.

As I wrote in the discussion forum I think the dnfdragora-updater is not guilty in the current restart/shutdown stuck issue.

The appropriate part of the logs that accuses dnf5daemon-server is guilty. Take a look on the time gap between Apr 26 01:57:33 and Apr 26 02:02:03.

Apr 26 01:57:33 systemd[1]: firewalld.service: Deactivated successfully.
Apr 26 01:57:33 systemd[1]: Stopped firewalld.service - firewalld - dynamic firewall daemon.
Apr 26 01:57:33 audit[1]: SERVICE_STOP pid=1 uid=0 auid=4294967295 ses=4294967295 subj=system_u:system_r:init_t:s0 msg='unit=firewalld comm="systemd" exe="/usr/lib/systemd/systemd" hostname=? addr=? terminal=? res=success'
Apr 26 01:57:33 systemd[1]: Stopping polkit.service - Authorization Manager...
Apr 26 01:57:33 systemd[1]: polkit.service: Deactivated successfully.
Apr 26 01:57:33 systemd[1]: Stopped polkit.service - Authorization Manager.
Apr 26 01:57:33 audit[1]: SERVICE_STOP pid=1 uid=0 auid=4294967295 ses=4294967295 subj=system_u:system_r:init_t:s0 msg='unit=polkit comm="systemd" exe="/usr/lib/systemd/systemd" hostname=? addr=? terminal=? res=success'
Apr 26 01:57:33 audit: BPF prog-id=70 op=UNLOAD
Apr 26 01:57:33 audit: BPF prog-id=60 op=UNLOAD
Apr 26 02:02:03 dnf5daemon-server[2401]: 2025-04-25T23:02:03+0000 [2401] DEBUG Metadata removal from repository cache in path "/var/cache/dnf5daemon-server/terra-2cbdb71aadff9295" complete. Removed 5 files, 1 directories (total of 731040 bytes). 0 errors
Apr 26 02:02:03 dnf5daemon-server[2401]: 2025-04-25T23:02:03+0000 [2401] DEBUG Solv files removal from repository cache in path "/var/cache/dnf5daemon-server/terra-2cbdb71aadff9295" complete. Removed 2 files, 1 directories (total of 803588 bytes). 0 errors
Apr 26 02:02:03 dnf5daemon-server[2401]: 2025-04-25T23:02:03+0000 [2401] DEBUG Downloading metadata for repo "terra"
Apr 26 02:02:03 dnf5daemon-server[2401]: 2025-04-25T23:02:03+0000 [2401] TRACE countme: no event for repo "terra": window already counted
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] WARNING Error loading repo "terra" (skipping due to "skip_if_unavailable=true"):
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] WARNING  std::exception
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "@System" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "copr:copr.fedorainfracloud.org:dsommers:openvpn3" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "updates" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "fedora" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "@System" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "fedora-cisco-openh264" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "rpmfusion-free" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "rpmfusion-free-updates" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "rpmfusion-nonfree-updates" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "rpmfusion-nonfree" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "code" with added file provides
Apr 26 02:02:05 systemd[1]: dnf5daemon-server.service: Deactivated successfully.
Apr 26 02:02:05 systemd[1]: Stopped dnf5daemon-server.service - DNF daemon.
Apr 26 02:02:05 systemd[1]: dnf5daemon-server.service: Consumed 1.041s CPU time, 323.4M memory peak.
Apr 26 02:02:05 audit[1]: SERVICE_STOP pid=1 uid=0 auid=4294967295 ses=4294967295 subj=system_u:system_r:init_t:s0 msg='unit=dnf5daemon-server comm="systemd" exe="/usr/lib/systemd/systemd" hostname=? addr=? terminal=? res=success'
Apr 26 02:02:05 systemd[1]: Stopped target basic.target - Basic System.


$ dnf info dnf5daemon-server
Updating and loading repositories:
Repositories loaded.
Installed packages
Name            : dnf5daemon-server
Epoch           : 0
Version         : 5.2.13.0
Release         : 1.fc42
Architecture    : x86_64
Installed size  : 643.9 KiB
Source          : dnf5-5.2.13.0-1.fc42.src.rpm
From repository : updates
Summary         : Package management service with a DBus interface
URL             : https://github.com/rpm-software-management/dnf5
License         : GPL-2.0-or-later
Description     : Package management service with a DBus interface.
Vendor          : Fedora Project


Reproducible: Always

Steps to Reproduce:
1. Just try to restart Fedora when dnfdragora-updater is running
2. In case everything is ok try yet another time because this issue is reproducable only in 80 - 90 % of times.
3.
Actual Results:
System is stuck for a very very long time or forever during the shutdown stage of the graceful restart/reboot process.


Additional Information:
As a workaround I disabled running dnfdragora-updater in the Startup Applications.