I get an error saying 'Error Code: 2013. Lost connection to MySQL server during query' when I work on Workbench. I increased the limit from 600 seconds to 6000 seconds. However, it loses connection way before 100 seconds. I'm using Workbench 6.1. My syntax has no issues with it since I tried on fiddle by creating a sample, small-sized table.
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You don't specify exactly which limit parameter you increased. According to MySQL documentation, It seems that the most suitable configuration option for this is
net_read_timeouton MySQL server (default 30 sec). Also, check the rest of the recommendations there.