/3/ - 3DCG

So I need to texture this backpack here for a game I'm submitting for a competition in a week. I don't need to bake or render it or anything, just export it as a .fbx. I've done this countless times already for other models using a "low poly" technique wherein I have a small (like 16x16) texture image with just a few different colors on it, and I use the Split UV's command in the UV Editor to separate the faces and then move them to the correctly colored region. But for some reason, I have several UV's on this mesh that belong to faces halfway across the mesh from one another, and the Split UV's command doesn't work to separate them. In fact, nothing under the UV Editor's menus has helped. When I try to Optimize or Unfold the thing in the Editor, it gives me this:

Error: Unfold3D command failed: Input polygon mesh data has unrepairable topology error(s)

So my question is, I suppose, how do I repair "unrepairable" topology? Do I really have to start this again from scratch?