Do you mean that the check was for the wrong amount, or that there were multiple accounts the check was written against, and one or more of them had the wrong amount?
If the check was for the wrong amount, you either need to cut an additional check (if too little was paid) or you treat it like an advance with excess funds. In the first case, make sure to note on both the original and new check what happened, and include the other check number and date for reference. If the second, the member should deposit the excess funds in a regular deposit slip, and you should deposit it into the appropriate budget category, and note on the original check what happened, and include which donation batch the refund can be found in and who it was from.
If instead you mean that the total was correct, but one or more individual categories was wrong, you simply need to view the expense and change the amounts to the correct ones. Instructions can be found in the RKATS finance article Changing an Expense Category