Since the Eclipse approach is different from the Designer approach (see Chapter 1. What is 1C:Enterprise Development Tools), the direct equivalent to the Save Designer command in Eclipse is Save All (on the File menu, click Save All). This command saves the changes in all of the editors, for all configurations.
To update a database configuration, use the Deploy configuration command, which is available on the project context menu and in the infobase list (the Infobases view).
If you choose an incremental update option (see Project editor) for a base configuration of a specific infobase and the base configuration update requires a user name and password, EDT treats clicking Cancel instead of providing the user name and password as a successful update. Therefore, it clears the list of objects changed after the last saving. If this happened, in order to prevent inconsistencies in the base configuration of your infobase, we recommend that you perform the full update of the base configuration. To avoid this issue, we recommend that you specify infobase access parameters that do not require any manual input during infobase operations. This EDT behavior is subject to future changes.