A couple times, I have seen SBS 2003 licenses disappear after a reboot. You're only left with the original 5 licenses. The consensus seems to be that antivirus scanning the licensing files is the cause. However, in this case, the license files were already immune from scanning. Anyway, here is a way to fix this issue:
1. Look for licstr.cpa & Autolicstr.cpa files under c:\windows\system32 folder.
2. Exclude these two files from being scanned by Anti Virus.
3. Make a backup copy of both the files on a different folder.
4. Delete licstr.cpa from c:\windows\system32 folder.
5. Rename autolicstr.cpa file to licstr.cpa.
6. Restart the Licensing Service.
7. Goto Server Management Console -> Licensing & you will have the actual no. of CALS.