Yours is an intermittent issue, one of the sort that is notoriously difficult to debug. There is an excellent page “B.5.2.9 MySQL server has gone away” to start from, in the MySQL documentation itself.
Intermittent occurrences of the same kind have been reported by means of the “random ‘server has gone away’ errors from GAE to cloud SQL” public issue tracker entry. You may consider reporting your case there. This may speed up the research for an eventual resolution or workaround.
Have you checked the values of your max_allowed_packet or wait_timeout parameters?
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