I suspect you won't be able to patch over the paint (whichever type you use.) You'll have to strip it down to the original outer coaing material, patch to that, and repaint. The bond between the paint and the original outer hypalon layer won't be strong enough.
For gluing the rubbing strake, hypalon glue is best, but regular contact cement works in a pinch (though it won't last too long.)
jky
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