Preheat oven to 400F.
Cut the eggplant in half lengthwise and rub the cut sides with EVOO. Place on a baking sheet cut side down and roast until tender, about 30 minutes. Let the eggplant cool until you can comfortably handle them then scoop the flesh out of the skin and into the bowl of a food processor. Pulse until pured and transfer to a mixing bowl.
Combine eggplant with the onion, garlic, 1 cup breadcrumbs, 1/2 cup Parmigiano-Reggiano, 1 egg, thyme, mint, lemon zest, salt and pepper. If needed, add additional breadcrumbs until mixture is moldable -- you can roll the mixture into balls now, or refrigerate the mixture for 30 minutes to make it easier to work with.
To roll the balls, scoop out about 2 tablespoons of the mixture, form it into a ball and flatten it slightly in the palm of your hand. Place a cube of cheese in the center and enclose the mixture around it. Repeat until all of the mixture is used up.
Spread out three dishes on the counter: Fill one with the flour, beat the 2 remaining eggs in another and in the third, combine the remaining breadcrumbs, Parmigiano-Reggiano and parsley. Coat each ball by running them through the flour, then the egg and then the cheesy crumbs.
When youre ready to serve the balls, heat about 2 inches of oil in a heavy bottomed pot over medium heat. Fry the balls until golden brown, about 2 minutes, then drain on a paper towel. Serve warm with Tomato Dipper.