Do not unplug an external hard drive without unmounting it first! I just had quite the scare when it looked like there were no files on the backup HD connected to my Raspberry Pi.
After some searching, I remember to search in journalctl and found out that it failed to mount via fstab, which is the thing that mounts what you tell it to mount every boot.
Running fdisk to find what the partition on that drive is called then running fsck on that drive's partition fixed whatever inode thing kept it from mounting.
One of these things had some message about the HD not having been properly unmounted, then I remembered yanking it out half an hour ago to try something.
I have a few needs that make the Pi (which runs Linux) the right executor for my backup system, but yeah, there are definitely some drawbacks here.