I have one per layer. Each layer with SCALE_AGL 0,... by itself flickers. But, if there's a higher-numbered layer without SCALE_AGL 0,... , everything seems to settle down. I have no flickering at all, now.What I do in ModelConverterX is put all the different layers in one BGL file. I then only add one empty SCALE_AGL command at the end of the area with all the different layers. Before I added one for each layer, but that indeed gave more problems
The layer numbers only seem relevant in FS9. In any case, I never had any shadow flickering in FS9. It was flickering of the ground polys - and only at night - when I added ground illumination with SCALE_AGL 0,.. on layer 8 that I had a problem.But I still have some flickering shadows now and then. I might need to vary the layer numbers as you mention.
Don
