WD My Book Essential 2 TB USB 2/3 1140 - problem with partially disappearing files

WD External Drives External Drives for PC
4

That is definitely not normal behavior, and suggests that either the drive or the MyBook enclosure is defective.  It may be about to fail completely.  I suggest backing up the contents to a different disk, during one of those periods where all the folders show up.

Then I would start an RMA claim with Western Digital.