No, You can not use Manual Numbering Sequence for importing new Sales Order, Customers, Customer Locations. Commerce Connector would import multiple records per minute so it has to be use Automatic Numbering Sequence for the smooth synchronization process. So please make sure you select Auto Numbering for Customer, Customer Location in the Customer Settings tab and Sales Order type that you selected in Order Settings of Stores page in Commerce Connector for Shopify and BigCommerce is configured to use Auto Numbering.
Can I use Manual Numbering Sequence for importing Sales Orders, Customers from Shopify or BigCommerce
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