In order to avoid duplicated listings there are a few things to ensure before enabling the auto-export feature to a store that already has products listed.
Upon connecting a new store to ExportYourStore, all active products you have on this store will be imported and matched against your source store products. The products are matched by their SKUs.
1. The products exists on both stores with the same SKU
If the product exists with the same SKU on both source and target stores, ExportYourStore will link them together. On the app they will appear as "Listed & Syncing".
Note: If you've just connected you stores to ExportYourStore, please give it some time to import all your products and mark them as synced/not synced.
2. The product exists on both stores with different SKUs
In this case, ExportYourStore can't recognize that this is the same product and may create a new product on the target channel with the source product SKU. This will result in a duplicated listing on the target store, one with the different SKU, and a new one with the source store SKU.
To avoid that, you can change the SKU on the target store and make it equal to the SKU of the same product on the source store.
Another option is to enable the "automatically close products that don't exists on the source store" setting, which will close all the existing products that can't be matched to the source store. Then if you have the auto-export feature enabled, the products will be listed again with the new appropriate SKU.
Note: If you don't use SKUs at all, ExportYourStore has a great tool to automate the SKUs assignment. Read here for more information.
3. The product exists on the target store but not on the source store
As long as you have the "automatically close products that don't exists on the source store" setting disabled, ExportYourStore will not update/change those products.