The uppermost take lane was soloed by me, not by default. I believe the bottom take lane was originally soloed. I did not find flatten comp in the Edit > History at the time I discovered this problem. The clip remaining in take lane 1 is identical to the the comp. I used Melodyne on track 48 after comping. I then recorded the output of Melodyne from track 48 to Aux 1. When that was completed I disconnected the Aux input causing the Aux 1 track to become track 49. I went looking and found that, yes, all of the takes are still in the audio folder. I suppose I could import those audio files back into my project.
I just tested this process in a brand new project and I can report with confidence that I was able to duplicate the problem. Everything was fine until I used Melodyne on the comped track. Once I used Melodyne all of the takes vanished and the Melodyne processed result now resides in take lane 1.