Hi.
I had a similar problem, not sure if it's the exact same though, these issues vary too much.
Anyway, I had two objects with two different UV sets, and I simply wanted to combine the two meshes with the UVs intact.
When I did, one of the sets would always disappear, which one depending on smaller circumstances.

I tried exporting them to .obj and all methods alike, and nothing worked. It wasn't until I selected all the UV-verts of both objects simultaneously, going into the UV editor, and hitting Polygons-Merge UVs, and THEN combining the two objects that it actually worked - but it really did.
Hope this helps you, and in any case, other people in a situation like myself, in fact I registered here just to make this one attempt of contribution with my experience.
Live strong!