it happens any time I install (or in this case, modify) a scenery to FSX.
Again, this shouldn't simply happen. If there's a problem with scenery.cfg, the scenery might not display, but the Addon Manager should't just disappear!
I've tried removing the relevant lines from the fsx.cfg file - it asks me to trust them, but addon manager never shows up in the sim. It seems the only thing I can do is completely remove the sceneries and reinstall them every time I install something else.
That wouldn't accomplish anything, except that reinstalling any of our sceneries, will get the current version of the Addon Manager, but you can also get it by installing the Stand-Alone Addon Manager, that doesn't requires to reinstall the scenery.
However, if the Addon Manager doesn't appear on the *first* launch after it has been trusted, it's not really a problem. It will appear on the 2nd launch, and if it doesn't then the problem is elsewhere, and it's an entirely different thing, which can't be possibly related to the sceneries installed and the scenery.cfg.
You simply had the wrong impression of this, because as soony you have seen the Addon Manager disappearing, you might immediately uninstalled/reinstalled the scenery, which wasn't needed, but then you tried and it worked, not because you reinstalled the scenery, but simply because you launched FSX another time.