Is there a way to manually adjust the elevation of a cell in the 2D mesh?
The only way I can think of doing that at the moment is to create an artificial terrain model from cross sections where i've input the specific levels and then overlaying this terrain and the original terrain.
There is no way that I know of to modify the elevation of a cell. However, there are some good suggestions about other methods of changing the terrain data in the following post: 2D modeling - modifying terrain/DEM.
I use a tool by Aris called Grid & Raster Editor within GIS that allows you to edit the individual raster pixel elevations. If you google aris you should find it. Relatively inexpensive.
I can usually edit the terrain file mapper is using and have it reprocess the 2D flow area to get the cell elevation to update but there are times you have to recreate the terrain file for it to actually update the flow area. When that happens it is usually with models that have more than 1 2D flow area.