We used Bamboo in evaluation version and upon final purchase of Bamboo the migration of the database requires a re-install. We already requested the license key with the old server-id. Now we do have a different server-id and it isn't possible to create a new license key.
There is no need to update the Server ID. The license was issued to a my.atlassian.com account, you can retrieve the license from there and enter it into machine B (see Updating your Bamboo license details). Once that's done and machine B is in production, you can decommission machine A.
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