Allow the cream cheese to come to room temperature before you begin. Combine the cream cheese, shredded mozzarella, sliced green onions, and red pepper flakes in a bowl. Stir until well combined.Drain the pineapple chunks as much as possible. Roughly chop them into smaller pieces. Roughly chop the sliced ham into small pieces. Add both to the cheese mixture and stir to combine.Place ¼ to ⅓ cup of the filling in each tortilla and spread to cover half of the surface. Fold the tortilla in half to close. Cook each quesadilla in a skillet over medium heat until brown and crispy on both sides.