I've had a scenario come up a few times now where I have had to change the arrival runway, which required a new routing on the STAR already in the MCDU. The easiest way to follow what I am talking about is look at KPHX and the EAGUL6 arrival. If, for instance you originally put in runway 8, the MCDU correctly adds in the way points/altitudes all the way to OBASE and adds in a discontinuity after OBASE for the expected vectors from air traffic. However, lets say the expected runway is changed to 26, there is now a new routing after HOMRR to JAGAL, with new altitudes and such. The MCDU will remove and replace the ILS way points for runway 8 with the 26 waypoints, but will not replace the STAR way points with the new routing required due to the runway change. The only way I've found to work around this is to completely change the STAR (runway doesn't seem to matter, and the best of my recollection changing the transition fix didn't fix it), insert the change, go back and reselect the original transition and STAR with the new runway.
The best I've been able to figure, this STAR/runway change is not specific to KPHX, but that was the easiest example I could come up with.