We also spotted these sql connections getting aborted, upon upgrading MySQL from 5.6 to 5.7. (Going back to 5.6 we don't see them!)
Turning on mysql general query logging we can see it is Dovecot's mysql connections that inquire about or update quota usage in particular:
*** /logs//mysql.log *** 2019-10-30T10:52:22.624690-07:00 2 Connect dovecot@localhost on npomail using Socket
2019-10-30T10:52:40.019780-07:00 2 Query SELECT bytes FROM quota2 WHERE username = 'a@bla' 2019-10-30T10:52:40.020948-07:00 2 Query SELECT messages FROM quota2 WHERE username = 'a@bla'
2019-10-30T10:53:40.113374-07:00 2 [Note] Aborted connection 2 to db: 'npomail' user: 'dovecot' host: 'localhost' (Got an error reading communication packets)
Increasing mysqld's net_read_timeout and net_write_timeout values to 3600 does not stop the aborted connections.
It seems asymptomatic. If the connection to mysql is still there to do quota operations, Dovecot seems to use it. If it's been aborted by the server, Dovecot seems to just (re)connect. . . But I'd love to help find the root or file a bug report or learn what it is we've configured wrong. . .
Benjamin