Ok. The thing is that Webinoly sometimes search for some specific patterns or string to replace or insert some data and configurations. If users modify this files unintentionally can break some features, for example, some #Comments in Nginx conf files are intended to be used as reference to insert or replace some strings.
Also, it's important to note that the best way to report a bug is only if you can reproduce it and explain the steps to do it.
Regards.