Hi sharky - unfortunately that's a big limitation of Blender - it doesn't deal with vertex normals properly and will discard them every time you go edit mode, even if you didn't edit anything that would require them to actually be recalculated.
That's pretty much a Blender specific problem, you could pretty much use any other kind of modeling program out there to avoid that happening.
Here are a couple of previous discussion threads about it:
http://moi3d.com/forum/index.php?webtag=MOI&msg=4256.1
http://moi3d.com/forum/index.php?webtag=MOI&msg=3583.1
http://moi3d.com/forum/index.php?webtag=MOI&msg=4424.9
If you must use Blender then Anthony's custom build that he mentioned above that fixes this is here:
http://chronosphere.home.comcast.net/~chronosphere/true-normals.htm
> Which applications or workflow can you recommend to achieve this?
As far as I know you can use literally any other program that can edit UV coordinates other than Blender.
> As the obj format is not that complex, another idea I had was to
> just copy the changed vt's (texture coordinates) to the orginal obj
> file or copy the original vn's (vertex normals) to the unwrapped obj
> file. But that didn't turn out well as the whole file seems to have
> been changed in between and they were out of sync. Is this feasible?
Yeah, that is probably possible, but you'll probably need to put only a single mesh object into each OBJ file that you want to edit this way.
I also wrote an OBJ merger utility that you can get here:
http://moi3d.com/wiki/Resources#MergeOBJ_utility
which was to help some people working this way of editing some separate OBJ files by hand and then having a way to merge them all together without losing the vertex normals.
You may want to look at a dedicated UV map editor program for doing this - there are a few choices for that:
UVMapper:
http://www.uvmapper.com/
Unwrap3D:
http://www.unwrap3d.com/u3d/index.aspx
Unfold3D:
http://www.polygonal-design.fr/
The first 2 are pretty inexpensive and I think there is also an older free version of UVMapper available on their download page, that might be worth checking out.
- Michael