do you mean the last option which says SDcard cleanup formats the card? In which case I am glad I skipped it as it seemed pointless getting rid of the "bootstrap" and "cias" folder, if that is indeed the only thing it deletes. I used my old SD card also and just renamed old bin files in case something went awry.
yeah, cleanup only gets rid of the unnecessary files. I'd keep the cias folder though or recreate it if u do the cleanup.