.well-known directory gone missing

I have four VPS running virtualmin, 2 on Centos 8 and 2 on Centos 7. All patched with up to date suggestions. Yesterday one VS failed to renew SSL. I noticed the .well-known directory on that Virtual Server was missing. I had to manually create it and the acme-challenge to make renewal work. I looked on other VS across VPS and the directories seem to have been wiped everywhere. Am I going mad or missing something?