We cannot send overpayments over to Xero. When a sale has an overpayment, handle all overpayments in Xero. Dear will download the payment of the invoice from Xero, but not the overpayment. 

Please follow the below steps to solve the sync issue:

1) Undo payment in Xero 

2) In DEAR, do not apply payment. Sync to Xero with no payment against the invoice. 

3) In Xero, record the payment of the invoice including the overpayment.