The problem is definitely coming from the Phone Link app. I got the issue back again today and all I have done since then was to disable phone link. I have tested this quite a few times and every time Phone Link runs in the background all MS apps close upon waking up. It doesn't really matter if you don't use Phone Link because it is set by default to start on startup. What I did was just disable it from running when my computer turns on and haven't opened it. You can also try to uninstalling it from windows features, but it doesn't really matter as long as it is not running. Just make sure to restart after you disable/uninstall. I would recommend those that are having an issue to give this a try. I am positive that this is the issue.
I also wish MS would take better care of these threads. It's frustrating that no one has got back to us. Anyways, give the above a try. I'll report back if the issue pops up again.