Hmmm, there is a small problem, if you don't include both quests, they're related to one another. My solution was the "ideal" line as I always did it. It's the logical way due to the quest log.
Encountering E in the final cutscene is triggered by having the letter in your inventory. If you report to Com. Ralph first or go to Hugh first after the final cutscene is not a quest buster.
Problem was, if I used the pyramids to get out of the cellar instead of going upstairs and reported to Com. Ralph.
Kiya
Hope, you have better luck this time, holding thumbs.
