It happened during the rolling restarts needed for a security upgrade (T138811).
It's still unclear what caused such flood in the logs but it's certainly the symptom of an deeper issue.
Create ticket upstream https://github.com/elastic/elasticsearch/issues/19187
If it happens again one can truncate the log file and restarting one of the affected node seemed to fix the issue.
FTR: I'll upload the logs to terbium under a folder named with this ticket id.