The condition of the Nefertiti bust was not fully understood until it was cleaned in Germany. What was known before export was that it was close to whole, but had no gold on it, and had damage (the missing eye, chipped ears).
The photos of all the items excavated were in black and white, which did indeed conceal what could be seen of the paint.
Regarding repatriation of these antiquities to Egypt, it's a bad idea. Imagine if you will there's another jihadist takeover as there was by Morsi (with the assistance of the Obama cadre) and the rioters again vandalize the museum.
For that matter, a few years ago a museum employee damaged the mask of King Tut and the first attempt at a fix was botched.
When I saw a reproduction of the Rosetta Stone, some years ago, it got me thinking, it would make more sense to have complete hologram reproductions of 3-D antiquities, to allow safer storage of the originals and to put them on display (even on demand) in museums throughout the world.
Palmyra.
Scan the objects and 3D-print exact replicas to be displayed in Egypt. The next time the museum is ransacked, send a new copy, etc.