Should I worry about my code getting overwritten Studio?

[jakobrosenberg]

Would it be possible to add comments to generated files that show which parts Studio will overwrite?

[Aurelsicoko]

The Studio only overrides the model file (ex: Article.settings.json) and generate new API folder.

[loicsaintroch]

No you don't need to worry about your code being overridden by the Studio. As @Aurelsicoko said the Studio only write your JSON models and config files with the default controllers. You can update your controllers as much as you want-- the Studio will never update them.