About the problem, do you think the server administrator could do something with your server?
That's not likely. It runs on AWS, and was donated by suchmoon (almost 5 years ago). I trust Bezos doesn't care about my little site, and if I wouldn't trust suchmoon I wouldn't have used this server in the first place.
I used to use hosting from local hosting sellers, and If I am not wrong, they had access to my server, and they have the backup. I don't know if they explore their customers hosting file managers.
The concerning part would be if someone else accessed it, but even then, removing some HTML files doesn't make sense. That leaves the possibility of me (or a script) messing up something without realizing it, which is also concerning. I don't know what caused it.