I've used data shortcuts and the promotion command to greatly reduce the complexity of merged surfaces with great success. In your case, I'd recommend the following method to help keep a workable surface. I've used this method to update an original survey with as many as 10 updated areas.
Create a new surface. Paste in the original surface, then paste the updated surface using the 'paste surface' tool under >Definitions and >Edits. If the new surface looks good, create a shortcut for this compilation surface.
If more updates are expected, you can isolate this surface to avoid too many edits on one surface that may bog down your computer. Open a new file, and save-as a new name. Create a reference to the compiled surface. Then simply 'Promote' the surface. This promoted surface has no edits, and is like a clean slate. But, contains all the data required to be the compiled surface. I generally will rename this surface in 'Surface Properties' to help separate it from the older versions.
This method keeps the surfaces simple and reduces the amount of work required for the refreshing cycles of Civil 3D.
Windows 7 64-bit
Dell Precision T5610, Dual-Xeon 2.6Ghz, 16 Gig RAM
Civil 3D 2013