Thank you so much!
So I have to comment here because of the Prestige Mod that I am playing with, and I'm pretty sure that I'm not the only one playing with this Mod
As the game was not originally created with the possibility that the farmer's Skill's Level will go backwards, when a certain Skill is prestiged, causing the Skill's Level to go from ten to zero, any recipes rewarded on the basis of leveling up are automatically forgotten by the player. For example, if the Farming Skill were prestiged, then the player will realize that (s)he can no longer cook Farmer's Lunch or craft Seed-Makers, Kegs, Preserves Jars, Fertilizers, or even Scarecrows. When these recipes are forgotten, then the game's built-in perfection tracker will "forget" that the player had once crafted those recipes. For example, in my current Stardew Expanded modded game, the tool that Odin posted above has indicated to me that I have "not crafted" Lightning Rods even though I already have 35 of them on my farm!
So my advice to anyone who is running the Prestige Mod but also wanting Perfection is to first complete every phase of the Perfection run with the exception of the Cooking and Crafting phases. Next, concentrate on cooking and crafting those recipes that are NOT awarded to the farmer solely on the basis of leveling up such as recipes purchased from or traded by NPCs, recipes learned through the Queen of Sauce, recipes sent by mail by NPCs with a high amount of hearts, recipes learned through certain Heart Events with NPCs, and recipes awarded for completing Special Orders of certain NPCs. Once these have been crafted, plan on a day that you intend to seriously strive for Perfection, and then when that day comes, do not prestige any of your skills until you have successfully crafted and/or cooked every remaining recipe, slept for one game day, collected all the items associated with achieving Perfection, and viewed all the Perfection-related cutscenes!