I’ve encountered this before as well, I booted a different OS from usb, but you could probably use the Qubes Installer rescue mode as well (UEFI troubleshooting | Qubes OS), then just manually find and mount the boot partition. Here’s a copy of the commands I’ve used to get a bootable install: (run as root)
mount /dev/the_partition /mnt/qubes mount the boot partition
cd /mnt/qubes/EFI go to the EFI directory
rm -rf BOOT
mkdir BOOT i just delete and recreate the directory to start clean
cp -r qubes/. BOOT copy all the files
mv BOOT/grub.cfg BOOT/BOOTX64.cfg rename the .cfg file
mv BOOT/grubx64.efi BOOT/BOOTX64.efi rename the .efi file
umount /mnt/qubes unmount the drive
Similar to what’s described in the UEFI Troubleshooting article, this will have to be redone after each dom0 kernel or Xen update, but it works for me.