This is not an ongoing issue, but it is something that I can't figure out.

My boss was trying to access our external RAID drive but it was not mounted. This is strange because it automatically mounts on startup and even stranger the computer is rarely turned off. To our knowlegde no one recently unmounted the drive.

Here's where it gets strange. The mount point: "/media/Book" was missing. Clearly the solution was to remake the mount point and remount, but why and how had the mount point disappeared?

Is it possible to have a "deferred delete?" That is I send a remove command which can't take effect now, but will take effect the instant it can. I've never come across that before.

Again not a pressing issue, just a curiosity.

As I known deleting of files is deferred if some programs has it opened. I tryied to recreate your behavior on Ubuntu, but rmdir on busy mount point is unsuccessful. I think mount points in directory /media are automaticaly created and deleted after use, but I didn't experience deletion of manually created directories within it.

You'll probably find anything under /media/ is dynamically created/destroyed by udev in response to a plug event. Umount a USB key, the mount point "goes away". That might imply the external had a "glitch" - I would schedule a fsck sooner rather than later.