Thanks for the reply,
I'm using wave ports as this is a simple form of coaxial line.
I've just tried your suggestion of de embedding the ports but it works as I'd expected.
HFSS models down the line from the reflectometer towards the source, then refers up the length of line specified in the de embedding (I specified the line length I'm modeling) so it ends up back where it started. I guess the is just to wind out the length of a port and get to a desired measuring plane.
Not what I'm trying to do unfortunately.
EDIT
After a bit of thinking and playing.
De embedding both input and output ports by the line length seems to do what i want, at least for a symmetrical line (plain line with a mismatch dead center). Just a simple problem so I can compare it with my analytical results.
I suppose it swaps the ports to the opposite ends of the line while the arrow of time stays unchanged.
Still working on it!
I've been using smith charts and maths for all my working life so I don't have much feel for these spiffy EM programs yet, probably looking at things in the wrong way.