Are you using SAML or LDAP for authentication? There are some behaviors with account enumeration with both of these that could potentially see accounts disappear (but their folders on disk should persist.)
Right, we do have occasional AD hiccups which result usually only in temporary disabled access, but in this case, the user accounts seemed to disappear from the SHs... does it make any sense?
Basically, if AD reports that no one is authorized, then their AD-generated accounts will disappear, and their scheduled searches will show as orphaned until the accounts catch back up. Does that match the symptoms?