Clear Books allows individual payments to be deleted off bank statements.  

Step 1.

Navigate Money > Bank Accounts and click on the required bank account statement.

Step 2.

Click on the individual payment to be deleted.

Step 3.

On the Payment Details page, click on the Delete button to the top right.

Step 4.

Finally, decide whether to just Delete Payment or Delete All.

What the terms mean:

Delete Payment

Removes the payment from the system and disassociates it from any invoice.

Delete All

Deletes both the payment and voids any invoices associated with it.