confirm successful transfer?

I work with content management systems a lot, and this means uploading and downloading a TON of little files spread across numerous directories. They usually take a while to transfer, even though the total size might be under 2 meg, it takes maybe 30 min because there are just so many files and folders making uo that 2 meg. On occasion, I have noticed that not all of the files transferred successfully, though I didn't notice any prominent message that told me the transfer had failed. There could have been a note in the log window, and I just missed it, but I don;t know.

What I want to know is, how does this happen, and what can I do to prevent it? Also, is there a way to confirm the transfer after it finishes? In Windows, when I copy a bunch of critical files from one drive to another, I do a to make sure both the original and the copy have the same number of files, folders, and bytes. Can Smart FTP do this? It would be a great feature - kind of like the 'verify disc when finished burning' checkbox in my CD burning software.