I know you all are busy... but, well, could you at least tell which part of C::B code could be responsible for processing project file paths?
And the issue might be not exactly Linux-specific. In Windows you can define NTFS-junctions to directories which work almost the same as symlinks in Linux, the only big difference that you cannot define an NTFS junction for a file while you can define a symlink to a file, linking directories works on both platforms. However, I haven't checked yet how a recent version of C::B deals with NTFS junctions.