Originally Posted By: tanstaafl.
Finally, I think I might have a clue as to what happened to the disappeared directories/files. My backup drive is a 2-TB drive in an external e-SATA dock. Something is not quite right with that setup, and on at least four occasions the computer has locked up during backup, forcing me to do a reboot with the backup software nominally still running. The dock can also use USB-2, and when connected that way I have never had a problem, so I have disconnected the e-SATA and switched to USB. I know that a forced reboot during processing can cause Bad Things to happen...

This is probably it. eSATA is pretty much the same as having the hard drive plugged in internally. Depending on how Windows settings were set, it was probably using internal drive settings that use write caching and other methods to speed up the drive. These settings are fine as long as you can guarantee the drive will never be removed when in operation (or ensure the system doesn't power off/crash), and time is given to safely flush any caches (in main RAM, on the controller in the computer, and on the drive) out to the disk.

USB within Windows defaults to assuming the drive may be pulled at any time. Less caching ends up being used, and more confirmation is done to ensure the data is written to the disk as soon as possible. It's slower (even when you ignore the speed difference between USB2 and eSATA), but much safer.