When it's set to False, the updater will handle the package addons like regular addons and won't delete the related modules when uninstalling.
Okay, perhaps phrasing it as a question did not exactly get my point through. I meant, it actually happened to me. I have HandlePackages set to false, and when !!!StandAloneLibraries has an update available (on "cmdau -up"), it WILL remove all the sub addons from the interface/addons/ folder that are not updated on the same run.
And this is also easily reproducable. For example, when I have all the addons up to date, just set the revision number in the updaters database for !!!StandAloneLibraries and for some other lib like "AbacusLib" for lower than they are. Run the updater normally with "cmdau -up" and I can see that it will update the "!!!StandAloneLibraries" and "AbacusLib", but mysteriously delete every other stand alone library from my interface/addons/ folder.
This is not related to only to !!!StandAloneLibraries, though. I tested it with Cartographer too, and it will remove all the cartographer sub addons from interface/addons/ folder if Cartographer is updated.
Though, I suppose I could just look at the source, and notice that the updater algorithm ignores the HandlePackages switch on uninstalling previous addon.
So updater uninstaller handles packages and never even takes a look at the "Settings.HandlePackages" switch, which is only looked at by the installer when actually installing the new revision.
Also, regarding the disappearing AllPlayed addon, I suppose it was some error somewhere. I notice that your updater isn't very big on notifying errors in the process (such as if the zip package failed to unzip or the package failed to download properly, etc...)
After trying this a bit more, here's a few things:
First time I ran it, it deleted my AllPlayed addon. No errors, no nothing. It just disappeared (it did add it to the revision database, though) (this was before my last post, though).
Secondly, does having HandlePackages set to False mean that instead of installing the packages, it uninstalls them? I have !!!StandAloneLibraries in my UI folder to check for new library downloads. However, if there is update available for the !!!StandAloneLibraries, the updater will remove every single stand alone library from my ui folder, that does not have update available on the same run.
Thirdly, it would be nice if the updater does not rewrite the log every single time. I was kinda thinking of running the updater as scheduled task, and it can be kinda bothersome to figure out if something went wrong at some point, because it destroys the old log every time it's run.