Heat a large skillet over medium-high heat and add the butter. Add the onions and cook about 10 minutes, stirring frequently, until softened. At this point you want to slowly add the pineapple juice, a little at a time, letting everything cook into the onions. Slowly add more until until you've added all the pineapple juice. Cook until the onions are caramelized to your liking and the pineapple juice has evaporated. Remove from the heat. Preheat oven to 350 degrees F. Roll out the puff pastry sheets and cut each sheet into 9 squares (18 squares total). Place squares on a piece of wax paper or parchment paper (this will prevent sticking). Brush the Hot Pepper Berry Bacon Jam onto each square of puff pastry. Divide the onion mixture among the 18 squares, top with ham and swiss cheese. Don't overfill, otherwise it will be very difficult to seal the edges. Brush egg wash around the perimeter of each pastry square and carefully fold dough over filling to create triangles. Pinch the edges closed to create a good seal. Generously brush the top of each turnover with egg wash.
Place on a parchment paper lined baking sheet.
Note: at this point you can freeze them to bake and serve later. Or bake and serve immediately.
Bake for 15 to 20 minutes or until lightly golden. Serve immediately with a sprinkle of chopped fresh thyme and flaky sea salt.