Preheat oven to 425º Fahrenheit. Cut two pieces of parchment paper about 2 inches larger than a 12-inch pizza pan. Have a rolling pin and a 12-inch pizza pan ready.
Prepare a double boiler. A sauce pot partially filled with water with a mixing bowl that fits on top will suffice. Over high heat, bring water in the pot to a simmer, then turn heat to low.
In the mixing bowl for the double boiler, add mozzarella cheese, cream cheese, almond flour, thyme and salt. Place the bowl over the simmering pot and stir constantly being careful not to burn yourself with the steam escaping between the bowl and the pot. A silicone mitt works well to hold the bowl.
When the cheese melts enough, that the ingredients hold together and it starts to resemble dough, dump out onto one of the prepared pieces of parchment. Knead a few minutes to mix dough thoroughly.
Roll the dough into a ball, then place onto the center of the parchment paper. Pat into a disk shape and cover with the other piece of parchment. Using the rolling pin, gently roll the dough into about a 12-inch circle. If the bottom parchment paper rumples, turn the dough over and straighten the parchment paper before continuing.
Place the dough and the bottom piece of parchment onto the pizza pan. Using a fork, poke holes all over the dough. Place pan in oven and bake for about 6-8 minutes, watching carefully. Remove when it is golden brown. Decrease the oven setting to 350ºF.
Sprinkle ¼ cup of the cheese over the flatbread.
Arrange onion slices.
Add the apple slices.
Layer on the ham pieces.
Cover with remaining ¾ cup of cheese. Sprinkle with the thyme, salt, and ground pepper.
Bake at 350ºF. until cheese is melted and crust is golden brown—about 5-7 minutes.
Remove the apple and ham flatbread from the oven and slide off of the parchment onto a cooling rack. Allow to cool for 2 to 3 minutes before cutting. Transfer to a cutting board and slice into 8 pieces.