My experience in the past: RTW from JNB bought thru a TA in Europe. Both credit in case of a return of the ticket or adding continents later was done in the original currency (ZAR) and then converted at the day of return/purchase the additional continents. The tickets were issued in ZAR.

Hopefully somebody else has more 'real life' experience. What is the currency AA is issuing the tickets in? That should be the currency for the refund.