Hi Babu,
If the invoice is posted with one currency and credit memo booked in other currency, in this case if you clear in any one of the currency, system will show exchange rate difference. This you have to post to the separate GL or if you are configured reason codes, then you can maintain the reason code and this will post to separate GL.
However, you can reverse the credit memo and post the credit memo in invoice document currency.
Regards,
Mukthar