If you want to list a product on eBay but make it unavailable in Magento store, you need to edit Product information in Magento.
Navigate Catalog > Products > Products grid and click Edit on the one you need. In General tab, you need to set Enabled in Status field and Not Visible Individually in Visibility field.
That's it. Now product will not be seen in Magento but can be listed on eBay. Orders for such products will also be imported.