All of a sudden AES (fs9) says Amsterdam is not installed or active
That's an AES issue, then.
so I go and re-install it (my reg key is intact), then I go to the airport and it's all messed up.
What do you mean with "messed up" ? As explained, many times already on the forum, when you have a problem with your activation, the scenery WILL STILL WORK PERFECTLY, it will just revert to Trial mode, with buildings disappearing after 5 minutes (and reappearing at the next sim start).
So, if your scenery was "messed up", the problem didn't had ANYTHING to do with the activation or the Addon Manager. If you had a problem with the activation, the scenery would revert to Trial mode. And if you had a problem with the Addon Manager not running correctly, you wouldn't see ANY scenery, not something "messed up".
I don't know what an FSX installation could do to mess up my FS9??? It's weird and I cannot seem to fix it now,. Both LSZH and EHAM are gone...
An FSX installation, in fact, should not affect the FS9.
I checked to see these are activated in the ADDON manager and they are but there is zero scenery in both LSZH and EHAM.
Now you are saying a different thing. It's "messed up" or it's "zero scenery" ? They are two entirely different things.
Both these airports were perfect before I installed JFK v2 in GSX and LAX in fs9 and FSX.
As I've said, that's entirely coincidental. Provided, of course, your copy EHAM was legit...I'm sorry that I have to ask this but, the ONLY case in which the installation of an FSX product would cause issues to your FS9, is if you had bogus/fake Serial Numbers in the registry for those sceneries so in that case, the scenery will disappear, since those serials would have been obviously removed by the new installer (the registry keys are shared between FSX and FS9) and in fact, AES will too report a problem with them.
The obvious solution would be reinstalling all your FS9 sceneries from the CURRENT installers, not from old installers you might have, they will work, in Trial or in Full mode, depending if your activation has been made correctly or not.