Urgent Windchill 12.1 upgrade question

While upgrading to Windchill 12.1 today, we required a reboot of the server. Windchill was running fine prior to the upgrade, but we could not access Windchill after. Windchill returned the following error "HTTP STATUS 404 Not Found": The requested URL was not found on this server. A search revealed PTC article  CS374085 which stated the cause of the error to be missing files 30-app-Windchill.conf and 20-mod_jk.conf in <HTTP_Server>/conf/conf.d Restoring those two files fixed the issue; I am just wondering what caused the files to go missing in the first place. Anyone have any experiance with this?