I think @Euwiiwueir is on to something, because it worked flawlessly for me some 12h ago:
user@dom0:~$ sudo qubes-dom0-update
Using sys-whonix as UpdateVM for Dom0
Downloading updates. This may take a while...
[...]
Dependencies resolved.
================================================================================
Package Arch Version Repository Size
================================================================================
Upgrading:
qubes-release noarch 4.3-6.fc41 qubes-dom0-current 68 k
qubes-release-notes noarch 4.3-6.fc41 qubes-dom0-current 11 k
Transaction Summary
================================================================================
Upgrade 2 Packages
Total download size: 79 k
DNF will only download packages for the transaction.
Downloading Packages:
(1/2): qubes-release-notes-4.3-6.fc41.noarch.rp 16 kB/s | 11 kB 00:00
(2/2): qubes-release-4.3-6.fc41.noarch.rpm 94 kB/s | 68 kB 00:00
--------------------------------------------------------------------------------
Total 65 kB/s | 79 kB 00:01
Complete!
The downloaded packages were saved in cache until the next successful transaction.
You can remove cached packages by executing 'dnf clean packages'.
Updating and loading repositories:
Qubes OS Repository for Dom0 100% | 0.0 B/s | 1.5 KiB | 00m00s
Repositories loaded.
qubes-release.noarch 4.3-6.fc41 qubes-dom0-cached
qubes-release-notes.noarch 4.3-6.fc41 qubes-dom0-cached
Updating and loading repositories:
Qubes OS Repository for Dom0 100% | 0.0 B/s | 1.5 KiB | 00m00s
Repositories loaded.
Package Arch Version Repository Size
Upgrading:
qubes-release noarch 4.3-6.fc41 qubes-dom0-cached 223.3 KiB
replacing qubes-release noarch 4.3-4.fc41 qubes-dom0-cached 222.9 KiB
qubes-release-notes noarch 4.3-6.fc41 qubes-dom0-cached 794.0 B
replacing qubes-release-notes noarch 4.3-4.fc41 qubes-dom0-cached 794.0 B
Transaction Summary:
Upgrading: 2 packages
Replacing: 2 packages
Total size of inbound packages is 72 KiB. Need to download 72 KiB.
After this operation, 413 B extra will be used (install 224 KiB, remove 224 KiB).
Is this ok [y/N]: y
[1/2] qubes-release-0:4.3-6.fc41.noarch 100% | 3.5 MiB/s | 64.4 KiB | 00m00s
[2/2] qubes-release-notes-0:4.3-6.fc41.noarch 100% | 272.9 KiB/s | 7.4 KiB | 00m00s
-----------------------------------------------------------------------------------------------------------------------------------------------------
[2/2] Total 100% | 2.1 MiB/s | 71.8 KiB | 00m00s
Running transaction
[1/6] Verify package files 100% | 400.0 B/s | 2.0 B | 00m00s
[2/6] Prepare transaction 100% | 16.0 B/s | 4.0 B | 00m00s
[3/6] Upgrading qubes-release-notes-0:4.3-6.fc41.noarch 100% | 5.1 KiB/s | 100.0 B | 00m00s
[4/6] Upgrading qubes-release-0:4.3-6.fc41.noarch 100% | 5.7 KiB/s | 100.0 B | 00m00s
[5/6] Removing qubes-release-notes-0:4.3-4.fc41.noarch 100% | 200.0 B/s | 2.0 B | 00m00s
[6/6] Removing qubes-release-0:4.3-4.fc41.noarch 100% | 34.0 B/s | 24.0 B | 00m01s
>>> Running %posttrans scriptlet: qubes-release-0:4.3-6.fc41.noarch
>>> Finished %posttrans scriptlet: qubes-release-0:4.3-6.fc41.noarch
>>> Scriptlet output:
>>> Running timer as unit: run-r743939128a014fbca02852ef5abd8136.timer
>>> Will run service as unit: run-r743939128a014fbca02852ef5abd8136.service
>>>
Complete!
So… happy days! 