It's highly unlikely that flourescent and non flourescent coral proteins would not break down once the tissue of the coral animal died/decayed.
Although not really applicable for what you are looking for, there is some great reading out there about coral pigment and responses to light which is very applicable to our reef tanks.
Tyree has an interesting take on it:
Reefs.org: Where Reefkeeping Begins on the Internet - View Document
He has actually shown some very interesting pictures of corals fluorescing very differently when photographed under different wavelength lights.