I tried separating the newly created faces and used a simple planar mapping on them. They look fine in the UV-Editor, but upon combining the meshes it again looks messed up.

The UV-Layout generated from the 3D-Scan is all over the place, i.e. there's one shell to the far left, another in the right upper corner and some more and the newly created one is connected to each one of them. I'd just need to separate the new faces to form a new shell which i can move freely in the UV-Editor.

Also I cannot redo the UV-Layout, everything is in place apart from these holes that need fixing. + I do not know enough about UVs.