Is it safe to edit Coursepress theme files?

When coursepress comes out with an update, will we lose any edits to the theme? I'm having to make a lot of customizations, so I need to make sure the changes will be secure into the future. If not, any insight into how to update Coursepress in the future to preserve any theme customizations is much appreciated. The plugin functionality itself is untouched, but we need to customize this theme in several areas in order to make it work for the current project.