There is almost no risk of losing your uploaded media. FTP transfers will only overwrite existing files, not delete them. Just don't delete the media files first. Where are you storing your media? I would recommend putting them in a different folder so you have no worries. For example, E:/Media.
I have upgraded my XBMC many (I mean MANY) times in the last three years, and never a problem. I got rid of some shortcuts in my settings once because I was lazy, so ended up just having to type them in again. No biggie.