I had this kind of problem once. No matter how I tried to merge the split edges, remove doubles etc. once it was imported to s4s the program split the edge again. (it was full body outfit and the split was created around waist and it definitely didn't need that split there). Never figured out how to stop that.
Hi. The program splits the mesh along uv island borders. The uvs are probably split. And if you're talking about a mesh split into meshgroups in random places, that is to interact with boots and accessories.
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