Nex Milkov
I reviewed the logic of Repeat and Near Repeat Classification tool, and the output lines are set to write to a feature class with Z Enabled:
The output points do write to feature class that is NOT Z Enabled, but it does write a "ZVALUE" attribute.
Here is an example of Elevation Layer Properties to visualize the points in a 3D scene:
Here is an example of Elevation Layer Properties to visualize the lines in a 3D scene:
With this combination you can achieve visualizations like this:
If the tool is creating output line features that are NOT Z Enabled as you've indicated then that is an unexpected behavior and we might need to take a look at the original input point data to help resolve the issue.