When you mark invoices as Sent you get the following prompt: Marking the selected invoices as sent will finalise them and disable editing or removing. Are you sure you wish to do this?
FlexiTime doesn't have any way of then reversing the invoice status back out. However it is something we at FlexiTime are planning on changing in the near future. You're probably best to manually adjust this invoice in Xero. And hold off marking the invoices as Sent until they're finalised and sent to the customer.