I've edited this thread because the understanding of the problem has changed. I originally believed it had to do with the type of raw file being edited. On further testing, I found that there's a new "Loading" display after a file is saved to .afphoto format. If the file is closed using Ctl-W or by clicking the "X" before that loading reaches 100%, the program crashes.
The steps to create this problem are (these are also in the current last post in this thread):
1. Open a raw file (PEF / NEF / DNG in my case)
2. Make no changes
3. Click on "Develop"
4. Make no changes
5. Save the file to .afphoto format
6. When the program is finished displaying the "Save document as" progress bar, press "Ctl-W" while the increasing percentage is being displayed in the "Loading" line above the image, to the left
7. The percentage display freezes, and roughly two seconds later, the program crashes