Denise, I am not familiar with the detail of a Kona, but believe that what you describe is a normal shockcord end part no. 71115001. You can undo these with a pair of needlenose pliers (or buy the Hobie tool screw in fittings part no. 71115101).
Once you have undone these, you can fit a new piece of bungee cord, tying a simple knot in each end and tucking the knot up inside the fitting, ensuring that the amount of bungee between the fittings matches the length of the original (or a little bit shorter if you want to increase tension, but I don't think you need to).
Then screw the fittings back into the hull. When you do the second one, the bungee cord will try and wrap itself into loops, but just go back to the first fitting you screwed in and jiggle the bungee until you can unwind the loops. In due course, you should have a brand new bungee which doesn't have a life of its own (LOL) and lies flat ready to be used to secure the hatch.
2012 Tandem Island "SIC EM"www.scenefromabove.com.au