Minecraft deleting itself when afk causing problems

Not sure if this is a one off

I was AFK fish farming on a realm and when I came back the whole of Minecraft has been deleted including all of my files related to minecraft. Haven't found a way to replicate this yet. After Minecraft was reinstalled, I was not invited by the realm and when I join it after being invited again, it says I am not white-listed even though I am.