You should test your site is fully functional on the test server before you begin an upgrade, as you have no way of knowing its functioning correctly before you begin. Then you should upgrade by uploading files over the original set. If you are not doing it in this manner, you are actually doing this in a manner differently to what is described in our documentation. If you are looking to 'clean up', that can be done after upgrading if needed.
So you should be able to uninstall on the test instance also. Note, we do not support 3.x in any way, so support time would not be relevant in this scenario also.