I hear that it's mostly XSI.

The mesh files themselves are just text, you can find them in the mod pack. No 3d software would be able to recognize them, I don't think. The file points to various textures the model uses, and those are the only changes I believe that people have done. I don't believe it's possible to reverse engineer any of the actual models, and I don't think ConvertData works backwards. This is an example from a .mesh file:

MeshData
hasValidTangents TRUE
BoundingRadius 351.123718
MaxBoundingExtents [ 219.822601 108.352074 322.265625 ]
MinBoundingExtents [ -219.822601 -107.640312 -316.303589 ]
NumMaterials 1
Material
DiffuseTextureFileName "CapitalPhaseBattleship-cl.dds"
SelfIlluminationTextureFileName "CapitalPhaseBattleship-da.dds"
NormalTextureFileName "CapitalPhaseBattleship-nm.dds"
DisplacementTextureFileName ""
TeamColorTextureFileName ""
Diffuse ffffffff
Ambient ffffffff
Specular ffffffff
Emissive ffffffff
Glossiness 30.000000

It lists 3 texture file names, as you can see, so you should be able to edit those. The rest of the file is hardpoints, and it looks like it lists all the vertices

Usually people are just creating a new mesh in one of the 3D programs (XSI), and then have the 'Entity' file point to it...

Someone did convert all the SINS capital ships to 3DS-MAX format though, I forgot where it was, but I saw it here somewhere...

Or you could just use ConvertXSI, in one the SINS mod packs!!!

http://janvanderweg.com/SOASE/

the XSI tools are horribly broken

get the 1.1 of this, it doesn't mess up smoothing groups