If License Manager does not reflect the truth about your licenses, and you can't amend it properly, start over.
First, using Control Panel / Services, scroll to the License Logging Service and Stop it. Then delete %windir%\System32\Cpl.cfg, %windir%\System32\Lls\Llsuser.lls, and %windir%\System32\Lls\Llsmap.lls. Restart the License Logging Service.
You should now be able to use License Manager to reflect your purchased licenses.