If S3D see the stl file has changed and you choose to update - the existing support structures stay on the build plate and the updated geometry is placed beside it. The support should be automatically removed.
I think a big benefit of this feature is that the supports are NOT removed! Basically, you can setup your entire print, but then if you realize you need to make a small change like increase the size of a bolt hole, you can update the STL file and it gets reloaded without changing anything else in the setup (placement, orientation, supports, processes, etc).
That being said, you can always reset the supports by clicking the Remove All Supports button.