External USB HDD no longer appears in File Manager mounted list, how to safely remove

If the disk has been unmounted, via Nautilus (using the eject icon), open the Disks application, select the disk to power down in the left pane, then click either of the icons marked below, to spin down the drive and power off, and then it can be safely unplugged from USB...

You can do this with hdparm:

0. Open Terminal (if it’s not already open)
1. Spin down the device:

   hdparm -y /dev/sdb
   

   ^{Note: Be sure to replace sdb with the actual device you’d like to spin down.}

You can use this command whenever you’d like to have the drive power down. If it’s mounted and an application wants to read from it, then the drive will spin up again.