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ClientSynq
QuickBooks tools

Replace invoices from a file

Enterprise plan

Last updated: October 8, 2026

Mode A of the Batch Modify tool replaces whole invoices in QuickBooks with the data in your CSV file. Each invoice in your file is matched to an existing QuickBooks invoice by its number, and every field and line item on it is overwritten. Use it when you have a complete, corrected version of each invoice.

To change only a few fields and leave the rest of each invoice alone, use Change specific fields on invoices or items instead. To create new invoices, use Import invoices into QuickBooks.

Before you start

  • You need the Enterprise plan.
  • Your role needs the Import to QuickBooks permission (Roles page, QuickBooks Tools group). Without it the page shows Access Denied.
  • QuickBooks must be connected.
  • Every invoice in your file must already exist in QuickBooks. Mode A never creates invoices.
  • Changes cannot be undone from ClientSynq, and Mode A does not keep a copy of the invoices it overwrites. To keep a record first, fetch the same invoices in Mode B, click Download CSV for Editing, and save that file.
  • Prepare a CSV file:
    • The first row must contain column headers.
    • One column must hold the invoice number.
    • Each row is one invoice line. Rows with the same invoice number make up one invoice, so include every line you want the invoice to keep.
    • Invoice-level values, such as customer and invoice date, are read from the first row of each invoice.
    • You must have columns for the customer, invoice date, product or service, and line amount, filled in on every row.
    • Dates must be MM/DD/YYYY or YYYY-MM-DD. Amounts, quantities and unit prices must be numbers.
    • Customers must match the customer's display name in QuickBooks. Products and services, classes and departments must match their names in QuickBooks. Capital letters do not matter.

Steps

  1. In the sidebar, click QuickBooks Online Batch Modify.
  2. Under Choose Your Update Method, click Mode A: Replace Entire Invoices.
  3. Under What type of records do you want to update?, click Update Invoices. Update Payments and Update Customers are not available.
  4. On Upload CSV File, click the upload area and choose your .csv file. Only CSV files are accepted.
  5. On Map Fields:
    1. If a saved template matches your columns, click Use This Template or Start Fresh.
    2. In the box "QuickBooks Online invoices will be identified using the Invoice number in QuickBooks Online", choose the column that holds the invoice number. A column named DocNumber, Doc Number or Invoice Number is picked for you.
    3. Under Fields to Update:, choose a QuickBooks field for each other column, from Invoice Fields or Line Item Fields. You must map Customer, Invoice Date, Product/Service and Line Amount. Leave a column as Unmapped to ignore it.
    4. Click Preview Changes.
  6. On Validation Results, check Total Rows, Valid Rows and Rows with Errors.
    • Tick Show only rows with errors to narrow the Data Preview. Cells with a problem are red and show the reason.
    • The Validation Issues table lists each problem with its row, field, issue and value. A required field you did not map is listed with the row Global, for example "Required field 'CustomerRef' is not mapped".
    • While there are problems, the button reads Fix Errors First and cannot be clicked. To fix a mapping, click Back to Mapping. To fix your file, correct it, click Back to Mapping, then Back, and upload it again.
  7. When there are no problems, click Execute Replacement.
  8. Review the summary Replace N invoices in QuickBooks. N is the number of different invoice numbers in your file, not the number of rows. Click Replace N invoices. Above 50 invoices, you must also type the count and tick a statement. See Confirm a large change.

Screenshot to come: QuickBooks Online Batch Modify Tool → Choose Your Update Method with Mode A, Mode B and Reclassify Account
public/help/tools/batch-modify-replace-1.png

Screenshot to come: QuickBooks Online Batch Modify Tool → Mode A Validation Results with summary cards and Validation Issues table
public/help/tools/batch-modify-replace-2.png

What happens next

ClientSynq shows Updating Invoices... with a progress bar, then Update Complete with Successful Updates and Failed Updates. Under Errors:, each failed invoice is listed by number with the reason.

  • Each invoice found by its number is overwritten with your CSV data, including every line item.
  • If QuickBooks has no invoice with that number, that invoice fails with "Invoice N was not found in QuickBooks." No invoice is created. Use Import invoices into QuickBooks for new invoices.
  • If a customer, product or service, class or department in your file is not found in QuickBooks, that invoice fails, for example "Customer not found: Name".
  • If more than one invoice in QuickBooks has the same number, that invoice fails. Fix the duplicate numbers in QuickBooks and run the file again.
  • Each invoice is processed on its own, so one failure does not stop the others.
  • ClientSynq does not email your clients.

If the run cannot start, for example because the count you confirmed no longer matches the file, you see a message and return to Validation Results. Nothing is changed in QuickBooks.

If you did not use a template, the results page offers Save as Template to save your column mapping for next time. Click Start New Update to begin again.

Good to know

  • Changes take effect in QuickBooks Online immediately and cannot be undone from ClientSynq.
  • For line items, ClientSynq uses Product/Service, Quantity, Unit Price, Line Amount, Line Description and Line Class.
  • The Batch Modify tool does not keep a history of runs on the page. Keep your CSV file and, if you made one, the Mode B download of the original invoices.