Source: 3D Mekanlar: Excellent brief history of Masjid Nabawi. For the 3D tour please click in the picture on the right upper flash picture.

Still does not fully explain what is happening to the other holy sites that may not be preserved due to latest expansion. But see below for more updated info.

Here:

Here is a post from Saudi Gazette that explains different models being pursued and it seems from this article that some effort is being made to preserve the historical sites, but Allah knows best. May Allah guide them to pay true respect to these sites.

See here