So, Here is my question. Why were the small ones hauling tail while the bigger ones stay down under the surface?
The first thing I'll address is the odor issue. A bad odor means you don't have a balanced black soldier fly colony as does the influx of other fly species. I think you know that already and you're now seeing the aftermath of the colony crash you described a few days ago.
Adding dry food items to dry the waste in the unit is fine if there isn't a bad odor. If there is a bad odor then I suggest that you stop adding any food at all. In that case I would use shredded paper (not newspaper or glossy) or sawdust (not pressure treated). Adding more food to an imbalanced colony will only make it worse.
The shredded paper or sawdust should be gently mixed into the waste, and to discourage other fly species you can leave a few inches of the paper in a layer on top of the pile. Most pest fly species want to land directly on the waste and the paper will discourage them. The paper won't hinder the BSF, in fact they may lay eggs on it so don't remove it from your unit.
Now for your question about the smaller larvae. I suspect these smaller larvae aren't BSF but are from the other fly species that have been attracted to your unit. A house fly larva can develop in a day or two and like most other fly species they're considerably smaller than BSF larvae. I imagine you have fruit fly larvae also. These other fly species will pass through your system in a few days. Just be careful about sanitation because some of these other flies carry pathogens.
