Interesting. I just test in my system, it works fine. you can try the steps below:
1. go to agent admin page, tab Application configuration, find your agent in the field Scope, go to the application com.sap.smd.agent.application.e2edcc
2. click Edit, then select the property, job.physicalhost.fqdn, click Remove Property,
3. remove job.physicalhost.ip as well
4. save the change
5. Edit again, use 'Add Property' to add job.physicalhost.fqdn and job.physicalhost.ip again. save the change.
6. go to LMDB, select hosts tab, then enter your host and check the FQDN.
Just ensure that you do the change for the correct agent which is really relevant to this host. You may try this for another agent as well to test it. It should work.