In the first instance you added an extra line into the running config. In second instance you only removed the line out of the config and uploaded it again. To remove a route you need to do a no ip route x.x.x.x etc. So if you'd put the word 'no' in front of the route you wanted to delete and then uploaded the config again, it would remove the line.
If you only just remove the line out of the config in NCM,it would work if you loaded the new config into the startup config and rebooted the router.