When you want to separate the building from the ground and put it in its own Region, then turn off the ground (do not delete it) and then select the building data that you want to separate out and place it in its own Point Cloud Region (away from the other buildings).
When you make your polygon select it says you have two regions (the Buildings and the Ground). Then you do your Keep In, all that is doing is showing you the data inside the polygon and hiding the other data so that it is easy to narrow down your selection process. If you select the part of the Ground region while it is visible in the Keep In selection, you are still selecting the entire ground point cloud region (hidden and visible parts) when you click on it and delete it, that is why it is gone when you do the Restore All because all that is doing is showing you the points that were hidden that are still left in the project.
Hope that this answers the question
If you want to "Delete Data" but be able to get it back, move it into a Point Cloud Region and hide it, do not delete it.
Alan