This seems not to work, I had the same problem.
This was my workaround:
- Create a new github organization repository and name it like your local project
- Open PyCharm and checkout the organization project into a directory different from your PyCharm project directory (if your local project with the same name lies there)
- Close PyCharm and copy all files and folders from the checked out organization repository into your local project folder
- Open your local project in PyCharm and add the .idea folder (with contains your PyCharm IDE project information) to the .gitignore file
- Finally commit and push your local project content to your organization repository!
- (Don't forget to delete the your former checkout folder)
This works because all git-paths are relative.