I am pleased to report that I received excellent response from Kevin Pinto and an individual in the SkyMiles department. Kevin replied the same evening and forwarded the issue to the/a coordinator of SkyMiles. She looked into the issue and responded the next day.

As for the "missing" miles, it turns out they were never missing. The problem is the activity report generated online. It shows a total of 400,000 miles being deducted and only 100,000 miles being deposited (instead of 200,000). However, when I check statements from periods before and after the original booking and subsequent change, the difference is about 200,000 miles (with some additional miles earned). So it seems like it is a Delta IT problem in reporting.