From your description above it appears that you are trying to call Visual COBOL executables directly from a Net Express main program. This may work if you are creating a new process using CBL_EXEC_RUN_UNIT in which to run the VC programs but it will not work if you are trying to call VC programs directly using the COBOL CALL statement.
You will need to recompile your entire application using Visual COBOL if the programs are being run within the same run-unit.