Yes. Pomona’s Pectin will start breaking down if it is subjected to extended cooking. After you have added the pectin to your boiling fruit mixture, you can continue to cook for up to 10 minutes without harming the pectin. After 10 minutes you risk breaking down the pectin.
An extended boiling water-bath of the filled jars also risks breaking down the pectin. The pectin is likely to be totally broken down by pressure canning. If you follow the cooking times in the directions and recipes that come with Pomona’s, the pectin will retain its full jelling power.