Preheat the oven to 375˚F (190˚C).
Place pitted cherries in a 9 x 13-inches ceramic or glass baking dish. Toss with light brown sugar and lemon zest. Bake in the oven for 17 – 20 minutes, stirring occasionally. Remove from oven and set aside to cool for at least 15 minutes.
Meanwhile, make the simple syrup. In a small saucepan over medium heat, combine sugar and water. Bring to a boil, stirring occasionally to melt the sugar. Remove from heat and set aside to cool.
Transfer the cherries with the cherry juice and lemon juice to a blender or food processor. Blend until smooth. Strain the mixture with a sieve to a medium bowl. Use the back of a spoon to squeeze out as much liquid as possible. You should have about 11-ounce cherry juice. Discard the skins & flesh.
In a medium bowl, whisk together the yogurt and ½ cup simple syrup.
Add cherry juice and sweetened yogurt alternatively into popsicle mold. Fill the mold until 90% full. Insert a chopstick or skewer into each mold and move around to create swirl. Cover with a mold lid. Insert popsicle sticks and freeze for at least 8 hours.
When the popsicles are ready, remove molds and serve. If the popsicles are stuck in the molds, dip the molds in warm water for 10 seconds or so.