I don't use Civil3D and cannot directly answer your question. However, I can tell you that HEC-RAS itself has a very quick way to flip the cross-sections from facing upstream to correctly facing downstream. Within the Geometry Data, simply go to Tools-->Reverse Stationing Data ... If you immediately click the Arrow, then OK, all cross-sections from all Rivers and Reaches will be flipped around. Only takes 5 seconds, and is probably quicker than the Civil3D flipper add-in anyway. Hope this helps...
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Robert Elliot P.E., M.ASCE
Senior Hydraulic River Engineer
Watershed Science & Engineering
Seattle WA
(206)521-3000