There is no user-functionality difference btween Pro and Advanced. The 'advance' features are all aimed at the developer. There would be no conversion necessary (unless you are using FM11 and want to upgrade to FM12).
If you are going to continue to develop, I'd push for 'Advanced'.
And any changes made to that file with FileMaker advanced--such as adding a custom menu or custom function do not prevent users from opening the file with regular FileMaker Pro and using it. The added capabilities will be fully functional, you just won't be able to change them with FileMaker Pro.