If you would like to reset the agent and clear all the files do the following :
$AGENT_HOME/bin/emctl stop agent
$rm $AGENT_HOME/sysman/emd/agntstmp.txt
$rm $AGENT_HOME/sysman/emd/lastupld.xml
$rm $AGENT_HOME/sysman/emd/state/*.*
$rm $AGENT_HOME/sysman/emd/upload/*.*
$AGENT_HOME/bin/emctl start agent
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