Okay, first of all, a point of terminology: DXT1, 3 and 5 are texture compression formats, they have nothing to do with the format of normal map used. The correct way to refer to the blue ones is "standard" normal maps, what FSO is using are "those damn special things taylor invented back in the dark ages for inadequately explained reasons".
Now, if you have a green normal map, you can convert it back to a standard normal map by copying the Alpha channel to the Red channel, then blanking or removing the Alpha channel, you can then feed this back into whatever method you use to reconstruct the height map (You may also need to flood the Blue channel with full color value, you'll have to experiment with this).