Stuck in Grub Recovery after installing Second OS to alternate Hard drive. How to recover?

[apparatus]

Untested, assuming /dev/sda is your Qubes OS drive:

cryptsetup luksOpen /dev/sda2 luks-qubes
vgchange -ay
mkdir /mnt/qubes
mount /dev/qubes_dom0/root /mnt/qubes
cd /mnt/qubes
mount /dev/sda1 boot
# Backup the /boot partition
cp -r boot root/boot-backup
mount -t proc /proc proc
mount -t sysfs /sys sys
mount --rbind /dev dev
mount --rbind /run run
chroot .
grub-install /dev/sda

After running grub2-mkconfig command below you only will be able to boot into Qubes OS.
If you want to be able to boot into your second OS as well as Qubes OS you need to copy the menuentries for your second OS from root/boot-backup/grub2/grub.cfg to /etc/grub.d/40_custom by following this guide:

Multibooting Qubes

Introduction You should think carefully before dual booting Qubes on your box. Read the guidelines carefully. One problem is that when you dual or multiboot, even if you are using encryption on your Qubes installation, /boot is still unprotected and could be maliciously modified by the other OS, possibly leading to Qubes itself being maliciously modified. The other problem is firmware security - for example the other system could infect the BIOS firmware, which might enable compromise or spyi…

grub2-mkconfig -o /boot/grub2/grub.cfg
exit
reboot

If you formatted the /boot partition you may also need to regenerate initramfs (with dracut -vf --regenerate-all) and vmlinuz (reinstall the kernel package) files for your Qubes OS kernels in /lib/modules.