When you make your standard FTP backup, you're basically making a copy of your documents somewhere else, in this case, over FTP to a backup server, where there's a folder with your name on it where you can keep it. (See a previous post about this...

Making a copy is great when you make a new file or change an existing file:

A new file just gets copied up to FTP. It's a new file there too.
A changed file also gets copied. Depending on your settings, FTP might ask if it should Overwrite, or Overwrite all. This is FTP checking to see if it should overwrite your backup with the changed file. As long as you're copying TO your FTP (not FROM), left to right, you want to overwrite.

Where this system breaks down is if you move or delete a file:

If you delete a file, nothing gets sent up to FTP, since there's no file anymore. However, since you aren't overwriting anything, since there's nothing left on your computer to overwrite with, the old file sits up in your backup. This can be a good thing if you accidentally deleted something, since it's on your backup still. However, just copying your My Documents doesn't give FTP a way to know to delete files that didn't get copied. You're just copying.

If you move a file, it's a "new file" in its new location. Therefore, it gets copied to the backup in it's new location. However, it's also a "deleted file" in its old location. So the old copy just hangs out there too just like the previous example. This really isn't a good thing in any scenario.

Like backing up in general, none of this matters until you have to restore your backup if your computer dies, and your backup becomes the only copy of your electronic work. If you restore with all these deleted and moved files every which where, you are well on your way to insanity and disorganization. So what do you do? Make a clean backup.

I only do this after I make substantial changes to my documents, because if you tried to keep up all the time, you would drive yourself equally insane maintaining two sets of your documents. I also explain this with a disclaimer to be careful when doing mass file moves via FTP - It is easy to delete things and User Services will smack me around, hard, if you tell them I told you to do this and you deleted everything. But what I do on occasion is this:

Login to FTP and on the right/server side rename the My Documents to Archive.
Then I do my backup. This backup will take a long time, because when we renamed the backed up My Documents, we've told FTP that every file we're backing up is new. (FTP normally skips unchanged files...) However, when this is done, we have an exact copy of our documents - no phantom deleted or moved files. When you are done with this and you are sure it worked, you can delete the "Archive" folder.