Steps to remove the agents in 12c:
$AGENT_HOME/bin/emctl stop agent
cd $OMS_HOME/bin
./emcli login -username=sysman
./emcli sync
[oracle@oem bin]$ emcli get_targets |grep Down
Status Status Target Type Target Name
-------------------------------------------------------------------------
0 Down oracle_database db1.test.com
./emcli delete_target -name="db1.test.com" -type="oracle_database"
Query
=====
select TARGET_NAME,TARGET_TYPE,PROPERTY_VALUE,PROPERTY_NAME from mgmt$target_properties where target_name = 'db1.test.com'
no rows selected
$AGENT_HOME/bin/emctl stop agent
cd $OMS_HOME/bin
./emcli login -username=sysman
./emcli sync
[oracle@oem bin]$ emcli get_targets |grep Down
Status Status Target Type Target Name
-------------------------------------------------------------------------
0 Down oracle_database db1.test.com
./emcli delete_target -name="db1.test.com" -type="oracle_database"
Query
=====
select TARGET_NAME,TARGET_TYPE,PROPERTY_VALUE,PROPERTY_NAME from mgmt$target_properties where target_name = 'db1.test.com'
no rows selected