Not only Qubes but also Arch (as opposed to Debian, not sure about Fedora) loose their boot capability after a BIOS update which sets Secure Booton; a consecutive setting to off does not fix the following problem: no boot option exits anymore in the BIOS and the system becomes unusable.
MSI motherboards do not allow fixing the problem via:
I’m using the MSI Z690-A Pro with the Dasharo firmware, and was able to restore the boot menu using the EFI tools in the firmware.
I don’t know if the stock firmware has the same options, but I didn’t need to run any commands. In the BIOS, I could browse the EFI filesystem and select the file I want to load, and then I just added it to the boot options as the default. This restored my boot options after a firmware update.
The solution is rEFInd. It even executes from any external boot stick under Linux or Windows (manual). No configuration required and only takes a second. It finds any EFI files and presents them as an icon.
Qubes OS then starts fine after a BIOS update on MSI motherboard or when the boot manager gets lost otherwise.