Hello,
First;
- Click on "Recovery Deleted License File" under Admin>Licenses to see the licenses which have been associated with the first one. Select them and click on submit.
- The deleted licenses should now be correctly in the SEP manager.
If the issue continue perform the following steps:
1 - Stop the Service Manager.
2 - Make a backup of the folder "C: \ Program Files \ Symantec \ Symantec Endpoint Protection Manager \ Inectpub \ License".
3 - Delete all files in the License.
4 - Make a Repair in the Manager through the Add / Remove Programs
5 - Import the license file again.
If the issue continue only try recovery license again.
Again, this issue seems to be Resolved in the Latest SEP 12.1 RU1 MP1 version.
Hope that helps!!