When a file failed to be downloaded during the auto-patcher, copy the file name somewhere (notepad, electronically or physically), then go to the following FTP site to retrieve it.
It is very possible that they will block directory listing in the future. This isn't the case right now, but when they do, just add the exact file name to the end of patch/ and you'll be fine.
Do not worry about the validity of the above site, because that is what the auto-patcher uses (This is iRO btw, be careful if you aren't using iRO).I would also recommend using a download manager, like GetRight, to resume the download when it fails, and to speed things up.
Now, to make sure you don't have to re-download certain files that gets deleted, first save the file you just downloaded to a backup directory, then copy it to the RO base directory.
This is usually located at C:\Program Files\Gravity\Ragnarok Online\
I've noticed almost all .RGZ files get compiled and deleted. Some of them are quite huge too. Every time the auto-patcher fails, get the new file that failed, and re-copy everything from your backup directory to the base RO directory. When it prompts to over-write a file, say NO. (Obviously the file wasn't deleted. It's the exact same file, so why waste time?) Keep doing this until the patch finally completes and repacks the main data file, and the game will then start.