Application to transactions

I have got an interesting requirement. We have transactions (invoices) which has freight and charges. The receipt should get applied in the sequence of charges then freight and then the line amount. So application rule set is defined accordingly and put into the respective invoice transaction type definition. This works perfectly fine as per our requirement.

Now, sometimes the situation arises, that we need to reduce the line amount. Since we can not change the invoice (as it has become unable to incomplete), we create a credit memo and apply to invoice. But the credit memo gets applied to freight and charges as well. I tried defining various application rules and add to Credit memo transaction Type definition but it seems that the invoice transaction type application rule prevails.