You must provide a receipt for all money they have GIVEN you. You also legally have to claim all money given too you. So write one for all fees paid. Mail it (registered mail, so they have to sign for it). You can write off the money still owing to too with your taxes.

From now on I would do
Payment in advance. No payment = no care until paid

I would communicate via email only, so there is a record of what is being said.
I would write:
To X
I have prepared your tax receipt for the amount you have paid. Once I have received the outstanding balance of $XXX, I will issue you a receipt for that amount as well.

If you would like only one receipt with the full amount, send me an etransfer for the outstanding balance to the following email account: email address; by 5pm on X day.

If I have not received your outstanding balance by the above date and time I will mail you the receipt for just the money you have already paid.

Thank you for your time
X