to the none of observant that would be a bit of a shocke to the system to come back later and find that 20% of your files are missing. However, I think this is more the exception then the rule.
When I do setup systems for clients, there is a check list to perform, which states to compare the size and number of files of the source with the distanation. Just to make sure that ever thing is coming over. And we do Copy and Move, then when comfirmed - the files on the source can then be deleted.
I take that it was on a Mac this happend, not that it can't happen on Windoze, but I have experiences something like this before and it had to do with the OS had locked some or many of the files, but would not alert to it. Never found a good explanation to this, other then from then onwards we would check all permissions first and correct these, then do the copy and varify. And I should mention, that it also had to be varified visually that the files were there, as in once it was estabilished that the number of files are there and the total size is matching. Then run through the directory structure and see if they match, randomly check a file to see if it opens.
This may be a lot mugging around, but it has saved my client several thousands of dollars, because she is relying on staff to check this and do these tasks - and it has happend that someone forgot and something went missing, which is why I got involved ;-)
Another reason for all this is also when you do move and finish a job and make multiple back copies, you want to make sure that its all OK, before investing the time to do so.
I'm not sure if Super Duper does verification on the copy, but it's a good idea. A few years ago, I transferred files from RAID to RAID, and in the copying I lost about 17,000 files. I simply dragged and dropped the files, and somehow about 20% of the 100k got corrupted. Luckily I am pretty conscientious about backing up and was able to restore them.
From then on, any copying of a large number of files is done with Chronosync with Verify Copy checked.