Reduce the apple cider: Pour 2½ cups apple cider into a medium saucepan. Bring to a boil over medium-high heat, then reduce heat to maintain a simmer. Cook for 20-25 minutes, stirring occasionally, until reduced to exactly ¼ cup. The reduction should be syrupy. Remove from heat and cool completely.
Preheat and prepare: Preheat oven to 350°F (175°C). Line two large baking sheets with parchment paper. Set aside.
Mix dry ingredients: In a medium bowl, whisk together 2¾ cups flour, baking powder, baking soda, 1 teaspoon cinnamon, nutmeg, ginger, and salt. Set aside.
Cream butter and sugars: In a stand mixer fitted with paddle attachment (or using hand mixer), beat ¾ cup softened butter, brown sugar, and ½ cup granulated sugar on medium-high speed until light and fluffy, about 3-4 minutes. Scrape down sides as needed.
Add wet ingredients: Beat in eggs one at a time, mixing well after each addition. Add apple butter, cooled cider reduction, and 2 teaspoons vanilla. Mix until fully combined, scraping bowl as needed.
Combine wet and dry: With mixer on low speed, add flour mixture in three additions, mixing just until no flour streaks remain. Do not overmix. The dough will be thick and sticky.
Portion dough: Drop rounded tablespoons of dough (about 1½ tablespoons each) onto prepared baking sheets, spacing them 2 inches apart. You should get about 24 cookies total.
Bake cakes: Bake for 11-13 minutes, rotating pans halfway through, until tops spring back when lightly touched and edges are just golden. Don't overbake.
Prepare coating: While cakes bake, mix ½ cup sugar and 2 tablespoons cinnamon in a shallow bowl. Melt 4 tablespoons butter and keep warm.
Coat cakes: Let cakes cool on pans for 5 minutes. While still warm, brush tops and sides with melted butter, then roll in cinnamon sugar mixture to coat. Transfer to wire racks and cool completely.
Make filling: Beat cream cheese and brown butter until smooth. Gradually add powdered sugar, beating until fluffy. Mix in 1 teaspoon vanilla. If too thick, add 1-2 teaspoons milk or cream.
Assemble whoopie pies: Pair cakes by similar size. Pipe or spread about 2 tablespoons filling onto flat side of half the cakes. Top with remaining cakes, flat side down, pressing gently. Refrigerate 30 minutes before serving for best results.
