Actually, all told, there's only 86 unique ships in there, and because so many of them are fighters or bombers, I'm well under the subsystem limit. I'll note that some wings get reused, but others only show up in one branch or the other.
The part that really sucks, and I mean really sucks, is updating the scripting. I built one branch of the mission before the rest, so now that I'm adding the second branch, nearly every event, right up until about the last two minutes of the ten to fifteen minute mission, needs to have its trigger updated. Some events, that seem like they'd be reusable, aren't because there are messages being sent from a ship that doesn't exist on the second branch. (I'm flirting with the idea of shoving some of those message lists off to chained events, but it's not always feasible.)
As for implementing new features in FRED, all I can suggest is another part to the tutorial, wherein you show the addition of a second branch to a mission like this, then have a picture of the author with his head exploded, to serve as a warning against such silly antics in the future.
Anyway, this really isn't all that much different from a mission that branches near the beginning and has two paths to the end. I just ran myself into a scenario, where the branch occurs before this mission, and I need to bring everything back down to one path. Much, much earlier in my time FRED'ing, I had made a stand-alone mission ("Too Many Secrets," if you want to go looking for it) that branched in the middle, so this isn't exactly new ground I'm treading on; the mission is just set up backwards now, with two beginnings and one end, rather than one beginning and two ends.
