If you still have the old server’s backup and you can get at the C:\windows\system32 folder, you “might” be able to restore the Service, rename “licstr.cpa in the system32 folder, copy “autolicstr.cpa” to Service and look in the Server Management Console to see if the licenses have been restored. If so, back those extra CALs up immediately with the licensing wizard and put the backup file in a safe place under lock and key.
As for why the licenses have disappeared make sure your antivirus software on the Small Business Server 2003 is not scanning the licensing files/folders:
The licensing files are located at:
Files and Folders to exclude from AV scanning both real-time and scheduled (assuming all programs are installed to the C: drive)
C:\Program Files\Microsoft Windows Small Business
C:\Program Files\Trend (substitute your AV program)
C:\Program Files\Trend Micro (substitute your AV program)