But what if the projectfile (*.cbp) has an UNC path ?
You mean if the project file itself is on an UNC path? In that case, there is no common top-level path and all files should use absolute file names / path's for all purposes. However, this is a very special case.
If you mean it contains files that are on an UNC path, these files must always be handled without simplifications, so there is no base path for them and also no relative path's. Those file should always only use the full path.
In the project tree they are shown as:
[ROOT]-[SERVER]-[FOLDER]-[...]-File.cpp
...while "normal" files are shown as:
[ROOT=BASE_PATH]-[FOLDER]-[...]-File.cpp