Hi Andrew, thanks for the question.

The case of the missing seed may have been solved. It seems a small fly lays its eggs in the flower and hatch out as orange larvae that take up house inside the fruit.   They basically turn the fruit into a gall by feeding and releasing some toxins which enlarges and fruit.  The seed doesn't develop.  Later they drop from the from the gall to pupate in the ground. The only control method suggested is to remove and dispose of the abnormal fruit before the larvae drop to reduce the population. Check out the following links:

Patrick Natale Kara Sousek chokecherry gall midge.pdf (unl.edu)

How to Grow Chokecherry in Your Garden | USU

I hope this is helpful.