Were the stones present in the heating of the preserve? If so, you may find that the flavor is a little deeper and more complex than you might have anticipated.

The reason I ask is that the pit of the sour cherry is what is used to make the liqueur Amaretto, so you might find this sort of almondy dimension to your preserves which, in my opinion, would be quite nice.

Just curious.

Sieve it! DonnyG is right on. The sieve will allow for a smoother and stone-free preserve.

If you have a sieve you can press the preserve through the sieve leaving the stones in the sieve and seperating the preserve in to a recieving dish.