If you are paying through an appointment and you Change or Delete a treatment in the purchase screen, this will disconnect that sale from the appointment. 

Meaning that when you pay through the sale, the appointment will not turn green and will indicate that it still needs to be paid through. 

If you are changing the treatments on an appointment this will need to be carried out in the appointment screen only. Once the changes have been made the appointment can be paid through. 

Appointment Already Paid Through

If the appointment has already been paid through and it is showing as grey or yellow you will need to Undo/Void the sale by going to Manager - Sales - Click the sale once - Click Undo/Void. 

Alternatively you could pay through the appointment and set the Price of the treatments to 0 so that the appointment is green and no extra revenue is taken as you have already taken payment for that appointment.