Hi Scott
I recommend switching off the Url Master module before commencing an upgrade of DNN. You can do this using the 'Friendly Url Setting' screen, 'Revert to Standard Provider' button.
After you have completed the upgrade, just click the 'apply changes' button again to activate the module. As long as you don't replace the 'dnnfriendlyurl' section in the web.config during the upgrade, your settings will be kept.
regards
Bruce