I remember when the originals were on display. I also remember when Traveler's skeleton was on display. (The school finally buried Traveler's bones right outside the lower level's door.)
A few more facts about those flags...
Two inebriated men decided to steal one of the flags. They managed to get outside, but they didn't get far.
The school gave one of the flags to either Tennessee or Kentucky some years ago. As Carl's article states, the flags didn't belong to the school - they belonged to The Museum of the Confederacy. I assume (but don't know) that the flag was returned.
I had heard that the school decided that the display of the flags would be more aesthetically pleasing if the (original) staffs were a uniform length - so it cut them down to size. A few years ago, I was in the flag room in the bowels of The Museum of the Confederacy, and asked one of the curators if that was a true story. He didn't say a word, but a very painful look crossed his face, and he stepped over to some long, skinny drawers where flagstaffs are stored, opened it, and pointed to a group of staffs that had been cut to the same length. I could tell it was a sore subject.
To try to answer Mike's question - the basement of the Lee Chapel contains a mausoleum where a number of the Lees are buried, Lee's office (as it looked that the time of his death), a gift shop, and a nice little museum. I'm sure the token exhibit flag (in it's "proper educational context", with apologies being issued right and left for those who might be offended, as well as a dose of apologies for slavery) will be in the museum.
For those who haven't been to Lexington - Stonewall Jackson's house can be toured, and Virginia Military Institute has a nice little museum (and a few artillery pieces on the parade grounds).