Sorry, NA - this isn't really an area of my expertise.
However, as I understand it: mixing static lighting (lightmaps) with dynamic lighting (vertex lights) is troublesome. When using a lightmap, you want the lightmap alone to define the lighting, which is why lighting is 'turned off' on a lighmapped level by making it fullbright. Having a lightmapped level also be affected by vertex lights looks plain wrong, I understand.
I think you need to come up with a different method to show the torch flicker. Apha'd decal sprites, maybe? I don't really know TBH - as I say, not really my area. :)
However, as I understand it: mixing static lighting (lightmaps) with dynamic lighting (vertex lights) is troublesome. When using a lightmap, you want the lightmap alone to define the lighting, which is why lighting is 'turned off' on a lighmapped level by making it fullbright. Having a lightmapped level also be affected by vertex lights looks plain wrong, I understand.
I think you need to come up with a different method to show the torch flicker. Apha'd decal sprites, maybe? I don't really know TBH - as I say, not really my area. :)