You can't exactly make a credit note for the tax only so you need to make a credit note WITH the tax and then create a new invoice without the tax. The customer now has a credit balance for the tax amount under the new credit note. 

  1. Make sure to complete steps 2-5 with the Contact --> Tax Exempt button OFF. The contact needs to be taxable for steps 1-3 to make a credit note with the tax.
  2. Open the invoice in Refund mode.
  3. Touch Credit/Return.
  4. Select the checkbox next to the specific item that was purchased in the original invoice
  5. Save the credit note to account.
  6. Make the contact tax exempt.
  7. Create a new invoice without the tax. If the customer is tax-exempt that happens automatically. If it is a one-off, then use the Pencil --> Override Tax to change the tax rate to 0.
  8. Use the Allocate Credit button to use the taxed credit note to pay off the new tax-exempt invoice.
  9. The contact will now have a credit balance equal to the tax amount from the original taxed invoice.

A similar procedure can be used toFix a Paid Invoice with Incorrect Tax