In fact, the Holocaust "bunkers", one of the items I was certain would remain, are completely gone. The 1940s "lifestyle" area is completely gone. All is different in the name of gaining more spacious visitor areas and more interactivity (but at the loss of authenticity).
One area that was better presented than before is the area that displays the acknowledgment of the State of Israel. There are items in and around the area, mostly gifts to Truman, that represent authentic artifacts from the ancient world - a Roman helmet, some pottery, and a scroll with a reading stylus. Prominent is a press release acknowledging and legitimizing Israel as a nation.
Another unchanged area is the little courtyard in the center of the building. Off to the side, visitors can still visit the office where the former president conducted business as the library/museum was being built. The office has been left in much the same condition to show what it would have looked like when Harry used it.
Outside of that are the graves of Harry, wife Bess, and daughter Margaret (and her husband). The graves are accompanied by a flame that constantly adds to the ambience of the area. My daughter and I made it a point to realize that this is as close as we will ever come to the 33rd president.