So, I merged some of the eXo's collections (eXoDOS and the likes) with my existing LaunchBox install. it comes with an "eXoPlugin.dll" that is supposed to go in the "Plugins" folder inside LaunchBox.
Well, THAT caused the issues I was having. After deleting this .dll from my Plugins folder, I can change the install status of all of my games and LaunchBox will not restore it to <Installed>false</Installed> .
That leads to further questions:
1. Why does the exo plugin alter all of my existing platforms that have nothing to do with the exo packs
2. Will eXoDOS still work without the plugin?
Well, anyway, I'm just glad I won't have to start from scratch. On the other hand, now I have to manually edit all of my over 400 existing platforms and delete the <Installed>false</Installed>. That will take some time, too.
Ah well, at least I know now hat was causing it...