I have read that if you need to uninstall a FSDT airport that you MUST say yes to both questions about uninstalling the add on manager and the other one which I can't remember right now.
Nowhere we said this. It's only done while troubleshooting an issue, to be sure no old files are left.
The only reason why you would want to remove the Addon Manager and the Couatl engine, apart from troubleshooting, is if you don't want to use any other FSDT scenery anymore, and you don't want to use any other product from other developers that use the Addon Manager as well, and want to get rid of unneeded files.
Also,if you say YES to this as you should, do all the other airports get affected?
They'll all stop working.
Which is why, the Uninstall clearly says "all the product requiring the Addon Manager will not work anymore", before getting confimation about removing everything.