Yeoman will see you have modified your files, and it will ask you what to do: you can overwrite them, see a diff, etc... I personally overwrite everything, and then use Git to see what has changed.
So a "normal" update shouldn't be an issue at all. For this next release, however, we have changed two things:
- Atmosphere is now optional, so if you don't choose this option, Yeoman will not be able to delete your previously generated files (you can't go wrong here, as your application won't compile if you keep the old files)
- The database data has changed (we added a new user), so Liquibase will complain if you already have some old data in your database (you also can't go wrong here, Liquibase will tell you about the issue)