The simple answer is, yes, layer information is lost once the FLA is compiled. There is absolutely no way to get any information about them at runtime. In that regard, there's not much you can do.
Your best bet might be placing groups of objects which were once on layers into container MovieClips. You can then give those MovieClips instance names, which could easily correspond to the layer names.
Otherwise, I'm not sure there's much you can do. Unfortunately, layers are a wholly Flash IDE-specific concept, and are essentially destroyed at compile-time.