Credit Notes and Reverse Charge VAT
You should be very careful when producing credit notes for goods to which reverse charge VAT is applicable.
The VAT code used for these credit notes should be the same as the VAT code used on the invoice that is being credited.
This is irrespective of the value of the Credit Note which is not subject to a de minimis test.
Duplicate
The easiest way to achieve this is to use Duplicate feature.
Duplicating and editing the invoice to create the credit note will ensure the VAT codes from the original Sales Order are picked up.
See Duplicating a whole Order to create a new Credit Note or Duplicating part of an Order to make a Credit note.
New
If you create a new transaction, you must be careful to select the correct VAT code.
If you create a new transaction the VAT code from the stock item will be selected (code V) and this may not be appropriate.
It will not be adjusted by the system because the de minimis test will not be applied.
The VAT code used for these credit notes should be the same as the VAT code used on the invoice that is being credited.
You will have to select the correct code by reference to the original invoice.