No there should not be a conflict with having Net Express and Visual COBOL installed on the same system as long as your system environment variables aren't set so that an incorrect copy of run-time .dlls would be located.
When CBL_DEBUGBREAK is called it will look in the system registry for the product of the run-time system in use and will locate the entry under the key [product-name]-->Config-->dynamic_debug_cmd_ptrace and will launch this command.
For the NX entry it will launch the NX IDE MFNETX.EXE. For the VC entry it will launch mfjitvs.exe.
As long as your application is compiled using a single product and it is locating the correct version of the run-time system cblrtsm.dll for that product it should launch the correct debugger.