SD card contents disappear when unionfs-fuse is introduced in raspberry pi

I encountered the same symptom.
In conclusion, there is a difference between the latest rasbian image as of March 4, 2017 and the information on the unionfs deployment site, so I think unionfs cannot be deployed as it is.
I also looked for a solution, but when the time ran out, I took care of ROMing by rebuilding the kernel with aufs.
Here are the details:

• Target Raspi Image
  2017-01-11-raspbian-jessie.img
• Workday
  March 2, 2017 - March 3, 2017
• Symptoms
  Deployed unionfs for reference to other sites just like the questioner.You can reboot for the first time, but not for the second time.

The part I looked up.

• In RAMDISK, /tmp is set to tmpfs, and I thought it might be bad, so I stopped.Also, I found parts such as /dev/shm that do not follow the current Rasbian image, so I made minor corrections.You can reboot repeatedly, but unionfs does not seem to work at all.
• When I run the commands in the script one by one with root privileges, I get the error that the parameters are different in the pivot_root instruction.We have determined that the reason for the failure to reboot is probably because the root system change is not working.
• In the meantime, the Raspi actual machine succeeded in building a kernel containing aufs, so the investigation was terminated.

That's all.

I became interested in the questioner's question, so
I tried installing it on archlinuxarm instead of raspbian

Install unionfs-fuse first, and

pacman-Sunionfs-fuse

Create two configuration files,

/usr/lib/initcpio/install/unionfs:

#!/bin/bash

build(){
    add_binary"/usr/bin/unionfs"
    add_binary"/usr/bin/unionfsctl"
    add_module "fuse"

    add_runscript
}

help(){
    cat<<HELPEOF
This hook uses unionfs.
HELPEOF
}

# vim: set ft=shts=4sw=4et:

/usr/lib/initcpio/hooks/unionfs:

#!/usr/bin/ash

unionfs_mount_handler(){
    cd/tmp
    mkdir-punionfs/root
    mount-oro $root unionfs/root

    mkdir-p/boot
    mount -- fstab unionfs/root/etc/fstab-oro/boot
    noprotect = 0
    [-e/boot/noprotect] & noprotect = 1
    umount/boot

    umount unionfs/root
    rmdir-punionfs/root
    cd/

    if [$noprotect=1]; then
        default_mount_handler $1
        return
    fi

    cd/tmp
    mkdir-punionfs/root
    mkdir-punionfs/rw
    mount-oro $root unionfs/root
    mount-tmpfs none unionfs/rw
    unionfs-o allow_other, use_ino, suid, dev, noneempty-ocow, chroot=/tmp/unionfs/rw=RW:/root=RO$1
}

run_hook(){
    mount_handler = unionfs_mount_handler
}

Configure /etc/mkinitcpio.conf to load the above and

HOOKS="baseudev autodetect modconf block filesystems keyboard fsck unionfs"

Initramfs image has been created.

 mkinitcpio-p linux-raspberrypi

It seems to be moving in general.No matter how many times I reboot, there is no problem.
However, in Denbndb's answer, there was an error in pivot_root, but
US>archlinuxarm uses the command switch_root instead and
Maybe this difference is why I'm doing well in my environment.

When it didn't work well, we did the following research.It's a prerequisite that shell works.

Try
• exit.Init may die and panic, but that's an experience.
• If you can't find ls while trying to run ls, try echo* instead.
Try
• mount-t proc proc proc /proc.
  You will be able to see the mount situation and use the ps command.
• If you know the PID of unionfs-fuse and can use /proc,
  cd/proc/PID/cwd allows you to navigate to the unionfs-fuse current directory.
  In other words, even after pivot_root, you can still see the filesystem that unionfs-fuse is looking at.

In the first place, raspbian and archlinuxarm seem to be very different, so
I wrote it as an answer in order to be helpful to some extent.