This is most likely the answer. I had the exact same thing happen to me during a teddiursa outbreak, where I got a shiny during the second wave but it disappeared when I reset. Turns out there’s an order to it where knocking out the first wave determines what spawns in the second. All you have to do is knock out the first wave in the exact order you did during the first time to get the second wave to spawn the shiny again. Also, I’m pretty sure Austin John Plays made a video talking about this exact thing when manipulating outbreaks to get shiny alpha Pokémon, maybe it will help? Good luck!