In most cases, if you successfully downloaded the images from the cameras to the hard drive of the device, the cameras will format automatically.
If something went wrong during your previous mapping run, this means the device failed to format the cameras, or the downloader didn't do everything automatically, this is not usually a problem. The only down side is the next time you download images from the cameras, it will take a little longer to download and sort them. The cameras have more than enough space on them, and your existing images will not be overwritten or modified.