There are two different options in CheckIn to remove an Invoice.
One is to Void the Invoice: this will retain a record of the Invoice, but remove all items and payments.
The other is to Cancel the Invoice. This is probably the better choice when an error has been made -- say, if an Invoice was created in error. This will remove the Invoice and restore the record to the previous status of an Order or SRO, and allow a new Invoice to be created.