The upcoming update will have the possiblity to start a new project with existing code. You will be able to import existing scripts together. This will overwrite the scaffolded script if required. For importing Ren'Py scripts, it now will also have Files or Folder import. 

One more thing: We will remove the single file export function, because we asked our testers if they ever use it....only 3% and even those who did in the beginning, don't use it anymore.