You can define filters in Sawtooth within the Data Management menu option. If you look in your Export Data option you have defined, you will see a Filter button which says "Respondents to Include" above it.
You can define filters, segments, etc. and save the commonly used ones.
I'm not sure this will save you a lot of time exporting but it's worth a try? At least it will only export the records you need on the 2nd run, 3rd run, etc.
In older versions of Sawtooth, this feature was not available which Eric is referring to.