I had assumed that Amazon was the problem with my incomplete version of Star Trek: Before Dishonor. Since it is currently $1.99, I purchased the Nook version, and it also cuts off in the same place (the end of Chapter 46). Judging from the sample contents of Google Play and Kobo, the problem is consistent across all formats. I sent in a customer service form with Simon & Schuster, but I have no idea if it will result in anything.
If anyone has newly purchased a version that contains Chapters 47-50, please list who you bought it from.