Manifest Zones are inheritly intangible. Floods would have happened before, and it's been here for a long time now. The reasons behind Manifest Zones appearing or disappearing are not well understood, but this one is apparently incredibly stable: the ECS says the towers have been growing for over two millennia, and the current Sharn has existed for 700 years (although that might change with an extra-bad conclusion to The Thirteen Cages
![Devious :] :]](http://www.enworld.org/forum/images/smilies/devious.png)
). It did, after all, take multiple artifact-level seals to shut down all the Xoriat Manifest Zones at the end of the Age of Monsters. The entire point of the adventure, after all, is that the floods are an annual occurance and the churches have ceased to produce the wands this year. Also, the towers aren't kept up by anything as mundane as foundations or something like that. The floating buttresses that are powered by the zone are what keeps them going up, not the ground.
Speaking of Teleport, that's also a Dragonmarked power, Orien's Greater, as well as Greater Teleport as the Syberis. In addition, the ir'Tains (hosts of the famous monthly Tain Gala, and perhaps the most influential of the noble houses) have industrial holdings down in the Cogs. They, at the very least, would move to protect their cash cows.
PS. The speed of delivery involved with the Airships and Lightning Rails also have to be considered. Although relatively speaking, by the time emergency order wands are done, it is probably far too late: it takes 3 weeks to make one, or 16 days with Exceptional Artisan. But still, I think you should arrange for something else small, vital, and magical to go missing.