The subject behavior will occur if you remove the secondary hard drive while the computer is in Standby or Hibernate mode.

NOTE: Even though the drive has been removed, Windows Explorer continues to display the associated drive letter, because an open handle exists on the removed drive.

To workaround this behavior, press the Safely Remove Hardware icon, in the Notification Area, and remove the secondary hard drive before your computer enter a sleep mode, or shutdown your computer prior to removing the secondary hard drive.