Combine the rinsed blackberries and blueberries in a heavy-bottomed saucepan over medium-high heat. Stir occasionally as they begin to release their juices, cooking for 10-15 minutes until the berries break down and become very soft. You'll notice the mixture will transition from whole berries to a chunky, jammy consistency as they soften.
Remove the cooked berries from heat and transfer to a blender or food processor. Blend until completely smooth, working in batches if needed. I prefer to pass the blended mixture through a fine-mesh strainer to remove the seeds, which gives the filling a more refined texture that works beautifully between delicate linzer cookies. Press gently with the back of a spoon to extract all the flavorful juice.
Return the strained berry purée to the saucepan and stir in the lemon juice and sugar. Bring to a gentle simmer over medium heat, stirring frequently to prevent sticking. I like to add the lemon juice early so its acidity integrates throughout the cooking process, brightening the deep berry flavor. Continue simmering for 15 minutes, stirring occasionally, until the mixture thickens significantly and reaches a jammy consistency that coats the back of a spoon. The jam will continue to thicken slightly as it cools, so don't overcook it or it will become too stiff for filling.