ok played it.... hmm... the behavior seems like you have the visibility settings wrong....
I had this and part 2 published since December 2011 or when the foundry came back up after season 5 launch. Why would I post this problem now, if you think that I did something wrong instead of 12 months ago?
Not to mention a Dev manage to replicate the problem before you came along.
If it's always the same pillars disappearing, then something about them might be bugged (could be some sort of state was set to them incorrectly, which you cannot fix). If that is the case, where it's always the same pillars, I'd suggest just deleting those and then replacing them with duplicates of pillars that you know work properly. That may fix the problem, although it won't fix the bug that caused it.
I saw what heppened too. I played it and yes, it works fine except the pillars disappearing. It's possible that one of the season updates messed it up somehow. I've seen it happen....
the behavior I saw is consistent with the pillars being set to be hidden once you get to a certain point. I'm not saying YOU did it... but... it's something to double check.
Becarful how YOU word it then, so it doesn't make it that it is the Author's fault.
Also with your review. There is a TNG episode that states about the weather control system on Earth were a Q interfeared with the weather or something along that nature. So there is really no sort of weather control system or provision mention in the Cannon Trek at all. Don't know what the episode is called though.
I also wanted to keep true to what happen in down in Queensland, Australia in December 2010, January 2011. Not what happen on a distant planet that have everyone on the planet speak Aussie.
I also found that it's pillars 7, 8 and 12 that consistently vanish. It is due to those 3, for some reason have been set to go Hidden upon objective completion. Switching those three pillars Visible to Hidden states to never and republishing should fix the problem. Why did those three suddenly change? I do not know. If changing the states of those three pillars and republishing doesn't fix the mission, let me know and I'll look into this again.
Also, while you're making those changes, I suggest moving the trigger volume for the generator beam down a bit further away from the generators. It is possible to over-shoot the spot and end up stuck inside the generator when it appears. An alternate but a bit more complicated option would be to put an invisible wall around the generator to stop a player from entering that space and then have the wall vanish after the generator has appeared.
That's really all I can do at this time. If anyone else experiences an unexpected change of an object's state settings, please let us know.