It may or may not be that Bogota's geographically anything at all like it is in real-life, by this point in the Sixth World. Folks enjoy belaboring the point because it's a way to keep poking fun at War![...]
Uhmm...you are the one who, instead of simply admitting an error, implies that War! is even worse than previously thought. Because if Bogotá dropped to sea level via MAGIC™, War! obviously missed that fact in the history section and the tactical implications thereof in the rest of the book.
[...]but the simple fact is shit changes in Shadowrun all the time, including the landscape, in some impossible ways.
The even more simple fact is that writers make errors. Occam and all that 
It's not my error, so I don't
really care too much (it obviously matters to me less than the people who keep bringing it up), I'm just pointing out that there's been an awful lot of mucking about with Momma Nature in Shadowrun's history. It's not my place to admit to an "error," when I'm not the one that may or may not have made it.
I'm not saying it's what happened with Bogota, because I don't know. I didn't write either book so I don't know if it's just genuine errors or if certain writers had something in mind. I wasn't even passingly involved with either of these books, so I'm just commenting as some dude that owns them and read them, not as any sort of "voice of the company" or whatever...but some folks complain about Bogota's jungle status in
War!, others complain about the passing mention of using a submersible to smuggle stuff in and out of Bogota in
Deadly Waves...and no one is coming up with ways to make it work.
I'm just saying it's a possibility someone can use, if they want to try and work something weird into their campaign, is all. There's a precedent for strange earthquakes, encroaching tidal waves, changing coastlines, and magical mountains that have grown or shrunk since the Awakening: instead of just bitching, people can try to make it work, if they want to.