if your clearing account is out sadly so are your bank recs. There is no way the bank rec is good when the withdrawl is not sitting in the banking gl and is in clearing gl. This is probably why you are thinking the contractor was overpaid as its sitting in two gl's.  

I would go back to May and pull your gl account for both the bank and the clearing and you will see duplicates. 

Then hoping you are on shared you can redo the bank recs back to May.  You will have to delete previous bank recs.  If the money is in both places means there is duplicate invoices created also. 

You will need to delete one of the transactions, if delelting the bank (1060 or whatever you use), and keeping the clearing account one.  You will need to do je to move from clearing into bank then redo your bank recs.