Hello.
Rules differ per country.
As example in Poland credit note has exactly same exchange rate as original invoice, so no exchange rate difference due to credit note.

Check if what customer say is really legally correct
Check if you have correct VAT law in Company info setting, so you do not test base on other country logic.
If legally required and does not work as should be write a wish and specify how system should calculate values in BC1 as in above case there is additional exchange rate difference involved.
Way round is to create CN not connected to original invoice, yes. But if any ex. rate differences should be calculated, this is extra manual.