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You should be able to ignore the warning.

In the official installation instructions, it says: "It is normal that [running local_setup.bat], if nothing else went wrong, outputs 'The system cannot find the path specified.' exactly once." I believe that it refers to the same warning, although the exact phrasing of the warning has apparently changed after the instructions were last updated.

See also a ROS tutorial, which says: "If you get an RTI Connext DDS environment script not found warning, you can safely ignore it in the scope of this tutorial."