Mauritzj - Yes, that workflow is VERY tedious. That's why I say Bentley needs to address this. Paul Brandl at PennDOT suggested importing the triangles into the DGN so that they would be fixed in place (see above). This is probably a simpler solution, although it basically makes the terrain less "live", if you know what I mean. Maybe that's a good thing. I think the workflow I've adopted still keeps the terrain model "live", for future work.
As far as flipping triangles, I guess we don't worry about that as much here. In the "old days" I worked for an aerial survey firm, where the "look" of the output was of utmost importance. That dated back to drafting days, and the fact that we were still trying to meet those visual standards. Here at MDOT, the attitude is more like, "so what if it's ugly, as long as it's accurate". Obviously this is an oversimplification, but you get the idea. While I might want to find and fix spikes and holes that shouldn't be there, I don't worry about the look of individual contours. As a photogrammetrist, my viewpoint has always been that if there's a problem with the triangles, then there's a problem with the underlying data. (Not counting edge triangles.) To answer your original question, no, it probably isn't practical to try editing your source data to get triangles to flip. Paul Brandl's method would preserve your triangle editing work in this regard.