There are various channel specific settings depending on the channels you are using in StoreAutomator.
This switch is located on the Channel>Channel Settings>Ebay Settings tab.
When this switch is enabled, SA automatically deletes unmatched variations from eBay. This is useful if you have encountered any mismatched variations. After that, you can override the variation options to create the relationship without getting errors from eBay.
IMPORTANT NOTE: Settings will be applied to all products with mismatched variations in selected eBay channels.