We don't allow duplicates.
Field crews have logs in each job folder, and they are supposed to record what point numbers they have used for field data collection. When the next crew goes out, they are expected to check the log, and make sure they don't reuse points.
For those times where duplicate numbers happen accidentally, we renumber the points in Excel before converting the CSV file to an FBK that we dump into C3D, since duplicate point numbers cause FBK import to fail.
These days, our field crews pretty much universally use linework codes, so we basically always use FBK import, and not direct CSV import. However, since we do a lot of GPS stuff, we don't really use the Autodesk-provided stuff much. Instead, we use a Perl script to convert a CSV file with linework commands embedded in the descriptions into a FBK, which we dump into C3D. Using this method, we basically cannot use any Survey Networks or any of that, but we've found much of that functionality to be superfluous in C3D. For the most part, we find that C3D's Survey Database is useless, since most of our jobs these days end up being a mix of conventional and GPS, and the Survey Database is GPS-clueless.