I could install Qubes successfully to my ssd and used it for over 1 week with no problems. then, when I removed the ssd containing qubes to format my windows 10 in the other ssd, I plugged the ssd containing qubes again and now qubes no longer appears in the boot menu in the bios, even though the SSD is recognized by the bios.
I have read the UEFI troubleshooting | Qubes OS (qubes-os.org) page and saw similiar threads describing the same problem, but I when I ran the commands instructed it gave me erros, I executed them on the shell in qubes rescue mode, in the installation medium. In the UEFI troubleshooting page it doesnt state where I have to run those commands, so I am confused.
You can ran them wherever you want (on any linux distro booted on that machine). This commands create new entry on your efi partition using tool called efibootmgr. But on that guide deoracted file is mentioned. For Qubes 4.1 You should use
grubx64.efi
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Also I remember using similar tool on Windows some time ago, so probably you can do it also from windows using similar commands.