It seems that the Tool doesn't care about the current content ModSecurity's config-file. The problem is that changes directly in the file are not noticed by WeBekci. Usually, such administrative tools always work with the current config-file(s). Is there a planned functionality to support this? If not so, I'm gonna write it myself, this shouldn't be too complicated.
Anyway, it's a nice tool, very helpful to avoid typing - and of course typing mistakes.