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If the install had already configured a repository, then yes, you would have to drop the existing repository before recreating the EM repository in that instance. See Oracle Enterprise Manager Cloud Control Advanced Installation and Configuration Guide: Using RepManager Utility for details on the dropall option. The EM nstaller will return a very explicit message if it finds a repository already exists, so I'm not sure exactly what steps you actually executed.
Thanks so much for your help! I was able to run the rcu to remove the tables needed, and do a fresh re-install with no probs. Thanks for your help on this.