That depends on what you mean by safe. If this is a production environment depending on those pages, no. But I assume you are still in development. The Ybos CMS adds functionality to the content-sections UI so you can specify that a content-section is managed by the CMS, so go ahead and replace those files.
Your best safety is to manage your development site with CVS. I just got converted to this religion. I was trying to take the easy way out, but if you control the site with CVS you can always go back to an earlier state. It also makes it easier to keep up with updates made to the core system after you have made changes.
