What you are experiencing is common for a pan style pizza store. First, there is no need to toss any dough out. Just remove any unused or over proofed dough from the pan and store it in the cooler until you make your next dough then incorporate into the new dough at a level not to exceed 15% of the total dough weight. This is also a good dough to convert to breadsticks or garlic knots. But that doesn't address your question; what I would propose is to manage your proofed dough (in the pan) directly from the cooler. Remove the proofed dough from the cooler, and place onto a heated shelf at 160 to 180F (anything close to this will work), think heated shelf for holding pizzas on for delivery or pickup. PVI used to make such a shelf but have discontinued it. Shucks! You could make your own with a piece of stainless steel and a couple of heat lamps under it. The idea is to allow the cold dough to set on the heated surface for about 2-minutes, then dress it and bake. As the overall dough temperature will be colder, you may need to experiment with baking using a screen under each pan to control bottom bake. There are several regional chains that use a similar process with good success. As a last resort, you can always par-bake your crusts too. This really works well for the deep-dish style pizzas. Par-bake the crusts using about 1/2 of the normal amount of sauce on the dough to control bubbling, depan, place on rack to cool, then store at room temperature until needed (should not be an issue with health department) to finish the pizza, place back into a pan, apply remainder of sauce, and dress to the order, bake with a screen under the pan to prevent over baking the bottom of the pizza. Can you say "crispy"?
Tom Lehmann/The Dough Doctor