Ah, right. Shan't be running this then! I only have 2 SD Cards, and I really don't want this to trash my stuff
You could just backup the data on the SD card you want to use. I did that with my regular second SD card when I made the video of Fruit Ninja/Angry Birds/Angry Birds Space, since I only had 3 SD cards (and the SD card I usually used for the Pandora didn't have a whole lot of space on it, not likely enough for the video).
But it doesn't seem to me it's erasing my cards due to "file/directory structure". In fact, it hasn't erased my cards at all. Are you sure it isn't due to the filesystem type, Neelix? All my cards are FAT32. Or maybe it's a problem that was fixed in r2?