Greetings! Thank you for your report.
The console should not be uninstalling games without your interaction. Is Destiny 2 the only games that uninstalls?
You may want to [url=https://www.bungie.net/en/Help/Article/12539]clear your console cache[/url] to see if that helps resolve this issue.
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This literally just happened to me as I was about to do the update for black armory. I'm furious. How the heck is that something that can happen? I dont get much time to play the game and now i have to wait an insane amount of time for it to install...this is ridiculous.