I have the same problem, I installed Qubes on an external SSD and used it normally. Yesterday, I wanted to boot Windows and removed the USB SSD while the PC was completely powered off. After replugging the Qubes OS entry isn’t appearing in the ROG BIOS Boot Menu (F8) or in the actual UEFI. What can I do to boot into my working Qubes install? Even Windows recognizes the partitions of Qubes OS.
Our issue seems to be related to Qubes suddenly cant boot anymore from external drive. Does that solve your problem? It describes the same situation of an installation on an external drive. Seems to be a firmware problem of our PCs. I will try it myself and report back.