Products that are enlisted in the eBay store can be removed from the shopping cart with the eBay end listing feature.
1. To get started, go to Products > Settings > Transfer Presets.
2. Navigate to Online Store Presets. Here you will see an option for End listing. Select the check box and choose the reason for ending your listing early. Then, click Save & Close.
Note: the above sync feature is only valid if the quantity is less than one, then it will be end-listed.