How can I maintain my Z values in my featuresclass using surface draper while replacing the vertices that lack a Z value using the surface provided?
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It depends a bit on the data. If the features themselves have mixed dimensions it's a bit tricky (for example a line with only some 2D points and some 3D points), however, if the feature itself is either 3D or 2D then it's pretty easy to just filter the feature which already have a good z value. You can probably use the bounds extractor to get a z value which you can then test for.
the ones which don't have a z value can go into the SurfaceDraper and the already 3D ones just go around it