When upgrading the application, you need to update to the latest release of your currently installed minor version (e.g. v2.0.2) before upgrading to the next minor or major version (e.g. v2.1).
Otherwise you may loose access to your data and need to wipe your database.
Also make sure that your custom applications using UpAndRunning2's API are up-to-date and are not using a deprecated API-version.