I've saved overtop of multiple backup copies, when I was cleaning up some of my scanned artwork. I was scanning them in at 600dpi , and on the computer at the time, I had 64 megs of ram - 2/3 of which was in use by the OS and such.. so each pic took almost 10 full mins to scan, then another 10 mins to save. I was saving to multiple locations so I could set up one to burn on cd in psd format, one fullsized jpg, then another at 1000px or so. I'd played around with colouring the one, including running a whole mess of filters that blurred out all the lines.. and then flattened it out and saved overtop of each one and closed out the file. I'd thought I was saving to a new file on each, but noooooo.
Not only was that hour wasted, but I didn't notice what I'd done until months later, when the scanner was no longer working - so it took almost 4 hours to clean it up.
yeah, we've all been there a few times.
 oh, and the new one is coming along nicely! i love the colours...