I take it that you saw “Match” in the Downloaded Transactions window and accepted it, only to determine that the match was wrong?
If that's the case and this happened “today”, resorting a backup from one day before “today”, if it's avalable, would allow you to redownload the transaction and get it correctly matched to the proper transaction.
The easiest way to undo this if you can't get a recient backup would be to delete transactions as needed, reenter them properly, and enter the “R” and/or “c” as needed in the Clr column for the transactions.