I found out my site has duplicate tracking code — Should I start over with a new GA account or just delete the duplicate?
Unless you have a good reason to delete a tracking code, don't
Assuming you are using asynchronous GA tracking codes, having one or two extra around won’t hurt anything. (Google doesn’t seem to mind, and they are footing the bill for the hard drive space, etc.)
You can just continue tracking on the old codes, in case it comes in handy one day. (Tracking traffic the same way over a long time can be useful.)
Reasons you might get rid of the code
You might want to take a tracking code off your site if you don’t know who else may have access to the reports — for example, if you are not the administrator for the given tracking code.
If the data captured is not accurate (say, your tagging was incomplete) you might want to remove the codes, so nobody will see the reports and become misinformed.