The plugin implements Google’s ecommerce tracking code for ‘universal analytics’ as described here:
https://developers.google.com/analytics/devguides/collection/analyticsjs/ecommerce
My understanding was that Google should take care of duplicates by itself since the plugin submits items based on their EDD transaction number. However, searching the web just now suggested that may not be the case.
I don’t seem to get any duplicates in my EDD sites though.
I’ll take a look if I get a chance soon, but in the meantime you could look at Yoast’s premium plugin for EDD/GA – which I believe now supports Universal Analytics. Let us know if that provides better protection against duplicates.
Another commercial plugin is available here: https://plugins.cminds.com/cm-google-analytics-ecommerce-tracking-for-easy-digital-downloads/
Just to be clear, I would never recommend using Google Analytics as an ‘accounting’ platform – but the ecommerce features might broadly help give some idea where your revenue comes from in aggregate.
I hope this helps, and I’ll let everyone know if I can find out more.