This is a case of SuperDuper out of control. I was investigating problems with a MacPro that had too much stuff on the hard drive. I launched Grand Perspective, a great app that gives a colored graphical representation of what files are on the drive and how big they are.
I noticed a large section filled with files that started with the path name of the backup drive. Now, normally Grand Perspective only shows the drive you ask it to inspect. I should not have been seeing what I was seeing. Tracing the path, it seemed that it started in the Volumes folder, an invisible folder on all OSX drives.
I made it visible using the widget "Hidden Files" and opened it up. This folder normally contains only aliases to drives plugged into the Mac, including the internal drive(s).
There was no alias for the backup drive. Instead there was a folder with the name of that drive and a second folder named the same but with a 1 at the end.
Switching over to SuperDuper and looking at the Schedule window I found five separate schedules, 15 minutes apart, two of which were in red. The backup was failing every time and I could not select the proper backup drive in its main window.
Somehow two of the schedules had pointed themselves into this Volumes folder and was dutifully backing up the internal drive onto itself in this invisible folder. The real folder had replaced the alias that should have been in Volumes and almost 400 gigs of files had filled it up.
Okay, delete. The first thing I discovered is you can't just delete from the Volumes folder. I would get a -8002 error if I even tried moving it to the Trash. Not knowing the technique to delete things in Terminal, I decided to enable Root and logged in as that. But the folder was invisible again. I tried installing the Hidden Files widget but it would fail to install! This was getting rather frustrating.
Okay, maybe it will work if I restart from my repair drive and log THAT into root and maybe it would let me install the widget there. I normally have Show Hidden Files always enabled when running from that drive so I thought, what the hell, I will try to delete those folders from here.
Surprise. It let me Trash those folders and then option-Empty Trash worked! I deleted both folders, one at a time, after ensuring that there was a successful TimeMachine backup in case my doing this destroyed the rest of the data on his drive. Not only did he have one, but Time Machine does not make copies of those invisible folders so I could have restored without also restoring the problem.
It takes a while to delete 385,000 files, even on a Pro. But when done, I ran Disk Warrior on the Pro's drive, which said it was okay. I restarted and not only did it boot just fine, with the almost 400 gigs of free space restored, but the Volumes folder now had a proper alias of the backup drive right where it belonged.
I created a new SuperDuper schedule and ran the backup and it went perfectly, with no failures.
The lesson for the reader here is that SuperDuper has a glitch that can get you in trouble.
Normally, when you set up the program, you click the Schedule button (after first defining the backup you want as a Smart Backup, not an Erase and Copy) and the window appears, followed immediately by a drop-down window that lets you pick the days and the time for the backup to run. This is how it should work, but the problem is after you create a schedule, the next time you click that button you get the same drop-down. What you must do there is click Cancel, then highlight the schedule script in the window and click Edit to make changes. If you just choose settings in the drop-down, it creates a second (third, fourth and so on) schedule, fifteen minutes later than the last (if you don't specify the time).
These extra schedules caused the problem, two of them having decided to install themselves in the Volumes folder. Then the schedules interfered with each other and the whole thing failed. So be careful when editing your schedule! It is okay to have multiple schedules, especially if you have a second drive with original material on it and you want SuperDuper to clone that drive to another backup drive (or second partition on your main backup drive).
There is a detailed PDF under SuperDuper's Help menu that tells you how to do all this and explains all the features, with pictures and descriptions. But how many users Read That Fine Manual?
Hint: I didn't read it either. I learned through trial and error.