Hello @schwesi
Be sure to upgrade to the most recent version of Zbrush–currently 2019.1.2. This is free for registered users, and comes with many new features and fixes. Obsolete program versions aren’t officially supported, and we can’t troubleshoot issues if we have to factor in potential issues with out of date software.
As to your issue, I’m not sure what exactly happened with the export, but it doesn’t matter because you didn’t actually fuse your mesh. (And by “fuse”, I’m referring to welding one mesh to another so that they become a single piece, not to the software being used). If you actually fuse the meshes together, this won’t happen.
When you merge two subtools together using the “merge” commands, you aren’t actually changing any geometry. You’re just re-organizing multiple meshes into a single subtool. A single subtool can contain multiple meshes.
To actually fuse the meshes’ geometry together, you will have to remove the head geometry that you want to replace, and close any resulting hole. Dynamesh can be useful for both. Then scale/move the replacement head subtool into the correct position. You can use either the above mentioned Dynamesh or Live Boolean to actually fuse the meshes into a single mesh.
Once fused there may be a bit of distortion or a seam around the area where the new head joins the body, since they wont match exactly. This may need to be sculpted and smoothed back into shape. If you keep the meshes fairly low poly like they are now, this should not be too difficult if you have basic familiarity with sculpting in Zb.
When you are happy with the shape of your mesh, you will probably want to clean up its topology with ZRemesher. As long as you remesh it into a fairly low polycount like it is now, it should remove most surface defects around the join area.
Good luck!