Preheat the oven to 350°F.
Line a half sheet pan with parchment paper. Break each of the Ghiradelli chocolate bars into 4 sections of 2 squares each. Lay each 2-square rectangle on the lined sheet pan, leaving a couple of inches between each rectangle. Lay one pretzel on top of each chocolate section. Turn the oven off and place the sheet pan in the oven -keeping the door propped open with a wooden spoon- for 3 minutes, or just until the chocolate is glossy and at least partially softened. Remove the pan from the oven and press the pretzels lightly; just enough to get them to adhere to the chocolate and close any gaps between the open spaces and the chocolate.
Let set at room temperature long enough for the chocolate base to firm back up. If you're in a hurry, you can place in the refrigerator or another cool place to speed up the process. Pipe or scoop the cold caramel into the "cups" formed in the empty spaces of the pretzel. Refrigerate for 10 minutes to allow the caramel time to settle into the divots.
While the caramel is distributing itself, melt the chocolate melting discs in a double boiler according to manufacturer's instructions. Set aside, stirring often.
Use a serving spoon to scoop chocolate over the caramel, covering the caramel and edges of the pretzel completely. Set aside to firm up for at least 10 minutes or refrigerate to speed things up. Examine them after the chocolate has set completely. If there are little holes where the caramel is escaping, cover them generously.
Melt the caramel chips in a double boiler according to manufacturer's instructions.
Use a fork to drizzle chocolate over the covered pretzels, then use another fork to drizzle caramel. Sprinkle with sea salt flakes, then repeat the chocolate and caramel drizzles. Let stand, uncovered, until firm. When the chocolate is firm set, transfer to an airtight container and store at room temperature for up to 3 days.