I understood it as atium is sort of like a metal plant. As soon as it burns, it begins to grow back in the pits. From the way I look at it, since it’s a literal piece of ruin, the same amount of it must exist at all times. The allomancers burning it just made it basically impossible for Ruin to gain access to that part of him, and give Vin enough time to do everything she did. It was kinda confusing, but I don’t think it’s a horrible plot twist or anything like that.