In a typical production environment, the amount of data you are talking about can be extremely large. A GUI tool like SWQL Studio would choke on that data just loading it into the grid even if the query itself didn't timeout. If you want to export all of your flow data, I recommend trying a different approach: iterate through the data by timeslices using a powershell script.
First, use SWQL Studio to write a query that selects a small time range of flows. Like this:
Select ApplicationID,DestinationIP,Packets,Ports,ProtocolID,SourceIP,TimeStamp FROM Orion.Netflow.Flows WHERE TimeStamp > '2017-07-26T12:00:00' AND TimeStamp < '2017-07-26T12:01:00'
That will give you one minute of data. Test it in SWQL Studio to make sure that it works and you are getting the data you expect. Adjust the time range so you are getting "reasonable" number of flows in each time slice. I would aim for around 10,000 flows - that should be a manageable chunk to work with. Assuming that works, then it is time to make the script. Let me know if you want a hand with that part.