Yep, been there, done that! For a while 1/2 the boats on Maui were missing their rear batten.
The instructions Hobie includes with the boat for tying the battens are not adequate IMO for when in heavy winds in irons. I knot the line on one side of the sail, then knot to the batten cap, then knot to the other side of the sail, and then cleat with a knot, and finally knot again to the first side sail grommet. Maybe not as pretty, but they haven't come off again!
Most people don't even notice they're missing. Sailing is fine without it, but may not point quite as high upwind.
Costs, about $10US each. They roll up for shipping.
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Hobie Island Sailing since 2006