You don't have to start over. If your update downloads say 400 files, those 400 files will not have to be downloaded again. Your progress is saved.
But remember there's a different between the Check File phase, Download File phase, and Install File phase.
This is correct, Checking the files is going to take the same amount of time everytime you have to do it but downloading saves your progress. If you have 20000 to download, and you get 10000 and then disconnect, you'll find you have 10000 to download the next time you try to Play the game. Also, since you seem to have trouble updating you may want to save the updated files in your ROM and Sound folders inside the FFXI folder. You can save those files to minimize the amount of updating you need to do in the future if you ever have to reinstall FFXI. An install plus update can take 3+ hours, but if you have them saved it can takes as little as 15 minutes.