I am not using Qubes R4.1 anymore myself. Whonix 16 on Qubes R4.1 still has security support, that is in the theoretic case that any security issues in Whonix code are discovered, these would be fixed.
However, I cannot run too many releases myself. I don’t know what changes were done in Qubes R4.1 which might have broken this. Qubes has more activity than I can keep up with.
Hence, if nobody can suggest a solution, this will probably remain unfixed.
Qubes dom0 updates is functional for me in Qubes R4.2 with Qubes-Whonix 17.
Upstream (Qubes OS) hasn’t provided a method to do so yet.
However, for better security and, at times, improved usability, it is recommended to perform a fresh start, especially with Qubes. This ensures that everything is presented fresh without the headache of issues that may arise during the upgrade process.