JDBC is unlikely to drop connections on timeout of 2 minutes (there is a default socketTimeout of 0 - never time out)
Is that a JDBC connection timeout or MySQL config issue? Can you run the same update operation through other means?
I suspect that you have non-standard wait_timeout and/or interactive_timeout values in your my.cnf config file for MySQL. Some people do that, especially for stateless apps. Defaults should be 8 hours though.
You can try configuring the Liquibase connection to mark it “interactive” for cross-testing, just set interactiveClient property to true – see if that makes a difference (which would mean that you should really adjust your mySQL wait_timeout)