1fireball,
What size SD card do you have? 2,4,8,16 or 32 GB? I doubt you have filled it up, but you may have. I doubt you are going to lose any data unless you delete all your nav data on the unit itself. The waypoints are stored on the unit. What I recommend is export all your nav data. It will be backed on the SD card. Then you can copy the files over to your computer. Give Humminbird PC a try, it is pretty good, and as long as you keep backup copies of your files, you should be ok.
What I recommend is reading up a little on specifically what you want to do and try different things. There are all sorts of tutorials and detailed instructions here and on the Humminbird website.
Lets get your Nav data exported and copied over to your computer first, then we can go from there with working with Humminbird PC etc.
Check out this post Exporting Nav Data with Waypoint management Software:
http://forums.sideimagingsoft.com/index.php?topic=4805Good Luck,
Robert