I think you should pick whichever game is more interesting to work on. Regardless of how easy it is to update one or the other, if you aren't really interested in the game it becomes a slog to work on. And if you find both interesting, it sounds like Nuclear Warfare has a reasonable codebase to start with, whereas Flee The Dungeon sounds like you'd either be building on top of spaghetti code or effectively rewriting a lot of the game. If that's the case then I guess you should work on the former if you wanna make new features, and the latter if you wanna refactor existing logic and make it easier to expand on in the future.
Overall though, I agree with Joels sentiment above.