I did a partial deviation a couple of weeks ago. My trip was revised to put a front-end DH that connected through my home city. It was inside the 60-hour window so I called CRS and requested to deviate on the first leg only but to keep the second leg intact. It worked as advertised - VIPS showed me as deviating on the first leg but second leg intact, as was GT.

You should be able to do this yourself outside the window. If you have any questions call your scheduler to make sure they know what you are trying to do.