The pictures of the waves are contained in files that are called .wov's. These files are contained in your default picture directory. Sonar limits the amount of space assigned to this directory, and when it gets full, Sonar will dump some of the older files to make room for new ones. Later, when you try and reopen one of these projects, Sonar will need to redraw the .wov's, which can take a long time. If you just wait long enough, the waveforms will eventually reappear.
You can also change how much space Sonar allocates to the picture directory, which will help reduce or eliminate the problem. The default size is 20 mb, I believe.
Find the file labeled AUD.INI in your Sonar directory, and open it in a word processor. Then find the line "PicCacheMB=20" and change the 20 to something larger (50, 100, 200 depending on how much hard disk space you have available). Resave the file under the same name. That should help ease the situation.