In my experience, once the mesh is generated, it seems to be it's own entity. Personally, I think this is one area where architerra is lacking, (although I have a email in w/ fabrizio to check this issue out further)
If changes need to be made to the contours I believe you will need to create a new mesh. I have never used the paint mesh tool from AT. I have found it much better to make a copy of the final mesh, trim it to the desired areas for roads/hardscape/......, then make another copy of that, and lower it 5" or what ever the thickness of your paving, and boolean it out. having a modelled road, rather than a painted on, saves you the trouble of repainting. Also, it shows much better in section, and is much easier to work out with the contours than slabs or roofs can ever do. until a feature is added to the mesh tool which would allow a controlled thickness, (I need to add that to the wish list)