If you are using Features module in Drupal 7 to deploy the rules. You will get an overriden or needs review flag in the Features UI when you attempt to turn the feature on. Features will see the existing code and it will not attempt to change it. Features is designed so that things done through the Admin UI of Drupal are not overriden unless you force Features to do so via a manual review of the feature.
To save yourself a lot of headache later on in the project I would suggest removing the rules before you install the Feature. Maintain configuration control with Features so that you know if you look at the Features admin page and a feature you have is showing as "overriden" or "needs review" then you have a problem on your website or someone has changed a part of the website. I personally have a website with about 20 features, all of them never say "overridden" or "needs review" if they do then I know another admin has done something that potentially should not have done.