As you can see the blue september folder has photos in it directly, there used to be several projects in the september folder, now just the folders are there with no projects. Also you can see that April, May, June also have no disclosure triangles next to them indicating they have lost their projects as well. Other months may be missing some projects as well. Also note the project caelyn books near the bottom, this had books in it but is now empty. Ever see anything like this?

If you have projects disappearing but not the images they contain, then you probably have selected Recent Projects at the top of the library pane. Change that to Show All and everything will be back to normal.

Recent Projects will show projects and blue folders that have been recently modified. What is confusing is that clicking on the blue folders will show images, and yet there can be no projects inside the selected blue folder to contain them. For example, I have 2005 selected and images are visible: