If you're data set is really big, the query will take a long time because Workbench is waiting for the Salesforce API to respond. With the first error, the query might have timed out, but Workbench let's the query run for 30 min, so somewhat unlikely (but not unheard of) unless its really, really big. Regardless, with something of this size, the Bulk CSV is the better way to go because it runs asynchronously on the Salesforce side as well. For bulk jobs, Workbench will keep refreshing until the query is completed, but of course it could take a long time. If you already closed Workbench, you can log into Salesforce and still get the results for (i think) 24 hours. Go to https://<your instance>.
salesforce.com/750 and see if you see the job results.