The microwave-safe side of a popcorn bag should be facing up during the popping process because the other side has a susceptor that soaks up microwave radiation.
Corn kernels are cooked when the bag’s internal temperature increases to the bursting point. If you put the kernels above the susceptor, they will pop more. They will also be fluffier and bigger. So, if you turn your microwave popcorn bag upside down, the only thing that will happen is that you will have fewer and less evenly popped kernels in the bag.
In other words, you can still have popped popcorn and the same taste even if you turn the bag of popcorn upside down, but you’ll have some unpoled kernels or “old maids.”
You can stop the microwave and flip the bag to the “proper” side. But don’t stress even if you don’t. It will still give you a bowl of tasty, crunchy popcorn.