as it is mentioned in the official release notes page (Oracle SQL Developer 4.0 Early Adopter Release Notes):
- The Check for Updates option to upgrade between releases of SQL Developer is not supported. This utility is provided to install third party extensions, this includes the third party drivers required for migrations and to add additional version control extensions.
- All new releases of SQL Developer require a full installation. Download and unzip the file into an empty folder. Ensure the "Use folder names" checkbox is checked when unzipping the file.
Migrating from Previous Releases
After you have installed the product you are asked if you want to migrate from a previous release. This migrates previously set preferences and connections created: By default the Confirm Import Preferences dialog that is displayed selects the latest installation. Select Yes to migrate the settings from that release or click the Show All Installations button to browse to an earlier installation..."
Hope it helps,