The update can't be finished when the database-server goes away. Find out why your mysql server closed the connection and modify the timeouts.
9.1.0 is out for a while now with a number of bugs that will be fixed in OC 9.1.1 which is expected in 1-2 weeks (also prevents db-timeouts on filescans, not sure about updates):
If possible I would wait for the 9.1.1 release. If you have the possibility to test the release candidate, this would be awesome, if your error still happens on 9.1.1, you should report a bug report.