minor: further fix race condition in refresh test

In the first test, test_connect_and_manual_refresh_with_secondary_down, I'm stopping only one secondary as opposed to all of them so that the primary doesn't step itself down and become a secondary. I assert that the number of secondaries has decreased by one after a refresh.

In the second test, test_automated_refresh_with_secondary_down, I stop the secondary that has been pinned for reads. Then I assert that the version and read pool change after an automatic refresh.