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How to Fix Inventory Sync Issues Caused by Duplicate SKUs in Webgility Desktop

Inventory sync problems between a store platform and systems like QuickBooks Desktop can often be caused by duplicate SKUs (Stock Keeping Units) in sales channel. When two or more products share the same SKU, it can disrupt automation and lead to incorrect inventory levels across connected sales channel and Quickbooks Desktop. This guide walks users through the process of identifying and resolving duplicate SKUs to restore proper inventory synchronization.

Step 1: Identify Duplicate SKUs

To locate duplicate SKUs in the product catalog:

  1. Run a SKU Audit
    Open the product catalog in the admin or dashboard view of the store platform.

  2. Export the Product List
    Use the Export or Download option to generate a CSV file containing all products and their SKUs.

  3. Sort and Filter for Duplicates

    • Open the file in Excel, Google Sheets, or similar software.

    • Sort the SKU column alphabetically.

    • Use conditional formatting or filters to highlight duplicate SKU entries.

  4. Confirm Whether Duplicates Are Valid
    Review each duplicate SKU to determine if it:

    • Refers to the same product (possibly entered more than once), or

    • Is a legacy or test entry no longer needed.

🛠️ Step 2: Resolve Duplicate SKUs

Once duplicates have been identified, take the following actions to clean up the catalog:

  1. Decide Which SKU to Keep
    Determine which product listing is correct based on:

    • Inventory accuracy

    • Sales history

    • Integration links (e.g., to QuickBooks)

  2. Delete or Rename the Duplicates

    • If the duplicate is incorrect or unnecessary:
      Delete the item using the product management interface.

    • If both entries are needed:
      Edit one of the products to assign it a unique SKU (e.g., by appending -01 or a descriptive suffix).

  3. Save Changes and Review
    Double-check that all SKUs are now unique before moving on.

🔄 Step 3: Re-Sync Inventory

After resolving duplicate SKUs, it’s important to reinitiate synchronization with connected systems.

  1. Re-download or Refresh Inventory Data 

  2. Run a Manual Sync to Verify
    Perform a manual sync to ensure:

    • No SKU-related errors are triggered

    • Inventory levels match across platforms