Tinaward, sounds like you might be attaching the reference as Relative and not full path. You can always set your MS_RFDIR variable to search for the right folder to look in. For exmample:
MS_RFDIR > $(CT_DIRPATH)/Aeronautics/
MS_RFDIR > $(CT_DIRPATH)/Project_Development/
DMS_RFDIR > $(CT_DIRPATH)/Construction/
MS_RFDIR > $(CT_DIRPATH)/Envir_Compl/