This is the standard set of actions that I go through when I have problems with an EM agent that a stop/start/upload does not resolve

The two types of errors I generally see are

EMD upload error: uploadXMLFiles skipped :: OMS version not checked yet..

Starting agent …………………………… started but not ready.

Follow the steps below, which can be cut and pasted

export AGENT_HOME=/app/oracle/agent13c/agent_inst

Stop the agent

$AGENT_HOME/bin/emctl stop agent

Remove the old log files from AGENT_HOME/sysman/log

Delete any pending upload files from the agent home

rm -r $AGENT_HOME/sysman/emd/state/*

rm -r $AGENT_HOME/sysman/emd/upload/*

rm $AGENT_HOME/sysman/emd/lastupld.xml

rm $AGENT_HOME/sysman/emd/agntstmp.txt

rm $AGENT_HOME/sysman/emd/protocol.ini

Start the agent

$AGENT_HOME/bin/emctl start agent

Issue an agent clearstate from the agent home

$AGENT_HOME/bin/emctl clearstate agent

Force an upload to the OMS

$AGENT_HOME/bin/emctl upload agent

Finally I sometimes need to re-secure the agent

$AGENT_HOME/bin/emctl secure agent

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