So I finally got a rant to tell, about me myself and I. Were working on my web host (personal gladly) and was trying to get ACME working without root access. I messed up and somehow got a folder named “~”, in a directory. I thought “well that folder is unnecessary” and I ran “rm -rf ~”. The moment I pressed “enter”, I realized what could’ve happened, and it did happen. My whole web-root gone. No backups. Just a big facepalm on my forehead ...
Take lesson, fix backups...