Warm the kefir in a small pot or in the microwave, just a bit so it’s not too cold (it’s okay if it separates on the sides). Add the yeast to it so it will dissolve.
Add the remaining ingredients to the bowl of a stand mixer fitted with a dough hook attachment. Add the kefir as well. Knead the dough for about 10 minutes on medium, until it becomes soft and tacky.
Set the dough in an oiled bowl, cover and set in a warm place to rise. After about an hour or two it should have doubled in size.
Preheat oven to 350 and lightly grease a 9 inch round pan.
Once doubled, punch your dough to remove air. Taking a small ball at a time, flatten the ball and place about two teaspoons of cream cheese in the middle then wrap the dough around it, pinch to close and roll it between your palms to make a perfect ball. Place the formed cheese balls close together and form a honeycomb shape into your pan. Once all the dough has been used or you have run out of space in the pan, cover the pan with a dishcloth and let the balls rest for about 30 minutes until they are puffy. Sprinkle with nigella seeds.
Bake for 20-25 minutes until the tops start to turn golden brown.
While the cheese honeycomb bakes, make your simple syrup by combining the sugar, honey and water in a small saucepan. Stir to mix then let boil until it starts to thicken and all sugar is dissolved.
As soon as your khaliya comes out of the oven, gently pour the simple syrup all over the khaliya making sure to cover all the balls and sides. Eat the same day! These are best fresh and warm.