I have a couple of ellipse curves which loft correctly with each other. I’m correctly extracting control points out of an ellipse curve, moving a number of control points using a domain, replacing those control points and creating a nurbs curve using those control points.

But after this process, these curves don’t loft correctly. I’d appreciate any help.

In this case If you create nurbs curve by using the control points of ellipse, then It’s not a degree 2 ellipse any more…
And since your ellipses are D2 curves, so they are not as flexible as you might think. That’s why I increased their control point count by using Rebuild Curve.
And also, If you’d like to preserve your original curve properties, It’s a good idea to use Nurbs Curve PWK.