The license assesment tool will look back at the history of the jobs to decide what options you used. By default it will look back a month or so, if I'm not mistaken.
But you can change how much history BELAT uses to make its report. I suggest you only let BELAT scan jobs from after the uninstall of the remote agents and the expiration of the ADRA option. Then check what it reports.
One other reason why BELAT may report too many remote agents is when a server is backing up some resources through the NETBIOS name and some resources through the FQDN name. BELAT thinks those resources belong to two different servers and will request 2 remote agents in its report. This is a known limitation of BELAT.