QB Issue Resolution:

The shipping fee is automatically transferred to the invoice when the progress invoicing feature is turned off. If you’re using this feature, you’ll have to manually add the shipping fee on the invoices.

 

This is the warning message you’ll get when an estimate has a shipping fee:

 

 

As a workaround, you’ll have to manually add a new service item for your shipping fee. You can follow the steps provided by MaryAnn. Then, add this item when creating an invoice. It’ll be included on the customer’s purchase list. You also need to make sure to identify if this service is taxable or not.

 

If you’re not using the Progress Invoicing, let’s go ahead and turn it off:

  1. Click on the Gear icon.
  2. Select Account and Settings.
  3. In the Sales section, uncheck the Create multiple partial invoices from a single estimate box.
  4. Click on Save.

Resolution for Issue 'Is there anyway to automatically bring over a shipping charge from an estimate to an invoice instead of having to manually re-type in the shipping?' available: Yes (Solved).
Source: Intuit Community forum.

Is there anyway to automatically bring over a shipping charge from an estimate to an invoice instead of having to manually re-type in the shipping?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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