A firmware update should not affect the encrypted container and you have confirmed it by unlocking and mount container in chroot.
This leaves the EFI boot partition which you also confirmed has been damaged.
I suggest you boot a live image and format the EFI partition
mkfs.fat -F32 -n EFI /dev/nvme0np1
Then open your luks container and mount on /mnt - then mount the EFI partition on /mnt/boot/efi, chroot into /mnt and run the Manjaro script install-grub.
//EDIT:
If the firmware update has removed grub from the firmware’s list of registered efi loaders - you need to run the efibootmgr to add the grub loader to the firmware.