We suggest copying the contents of the the old jdownloader\config directory over the contents of the new jdownloader\config directory. Just copying database.script is not sufficient, because there is an additional file of database settings.
Instead of saving the Links List as a .dlc, we recommend using Ctrl+B (Backup the database) or saving the links list using File -> Backup (or Save) -> Backup Links List. This saves to a JDC format that all you to specify the password and does not create problems on the jdownloader.org servers.
Using the Copy and Past approach will not work on links from a DLC file and will not preserve information about passwords (and so on). It is not recommended. We anticipate a new feature in the future to save the database as an XML file for local backup or for copying between computers.
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