Are you running cleanup cron jobs on the temp directory? If so, they've probably deleted the zip file sent to the agent. This issue will be fixed in Bamboo 5.0 - the jar file will be regenerated if deleted.
Until then you the only workaround is either to restart the server or reconfigure the /tmp cleanup.
I checked our plans and we only clear specific files (xauth and xvfb files) from /tmp. I have no cronjobs running that could do this either and looked through all users and the cron log. So, I don't think there's an automated process running that would clear this file.
Also, if I copy the file to the agent's tmp all is good
scp build@vmbamboo-01:/opt/atlassian/bamboo-agent-home/atlassian-bamboo-agent-installer-4.4.2.jar /tmp/jarClassPath6603717285566365500.jar
and see zero impact when I copy the file to server/master's tmp dir.
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