These are Qubes issue. See also Qubes/Update chapter Warnings.
I don’t agree with Qubes providing GUI (graphical user interface) based update tools if bugs (such as those linked in documentation) cannot be fixed in a reasonable timeframe. Exactly because error handling is bad. Pretty sure I raised this before Qubes implemented this (shared a link to Dev/Automatic Updates - Kicksecure) but was ignored.
Hence, this needs to be redirected to Qubes support as per What to post in this Qubes-Whonix forum and what not..