Foliage Painted on BSP is Deleted after Building Geometry

After painting foliage meshes on a BSP surface and rebuilding the level (more specifically the geometry), the meshes are deleted.

This bug is especially nasty because you cannot Ctrl+Z after building geometry and lights.

1. Create a blank 4.6 project using the first person template with starter content.
2. In the 'First Person Template' default level go into Foliage Mode and pull the static mesh "SM_Rock" from the Content Browser.
3. With the default brush values begin painting on the entire surface of the floor and the level until it is fully covered.
4. Click the "Build All' option.
5. Observe the rock foliage disappear.