I found this Rescue system (jumpdrive), chroot, luks and kernel updates (#306) · Issues · Librem5 / OS-issues · GitLab
saying that Jumpdrive can’t open LUKS volumes.
https://people.debian.org/~praveen/librem5-rescue.txt
This is a rough idea of how to chroot with qemu-aarch64-static. Setting up resolv.conf isn’t required in this case as you only need to use flash-kernel. First you need to free space on the boot filesystem, I don’t know what the best way to do this is, maybe removing the files by hand (vmlinuz, initrd.img, System.map, config, dtb symlink and subdirectory under dtbs/). I also think this warning in the flash-kernel manpage needs more investigation:
WARNING: Take great care when running flash-kernel in a chroot, since the choice of machine may cause host filesystem partitions to be mounted and modified.