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In a case where the Deposit is non-refundable and the Student is leaving your school, to properly recognize this, you can follow:
Create a "Forfeited Deposit" Catalog Item and set the GL Account to the a Forfeited Deposit Revenue Account.
Create an Invoice for this withdrawing family
Create a charge in the amount of the Deposit and post it to the AR invoice. This will Debit Receivables and Credit the Forfeited Deposit Revenue Account
Apply the Deposit payment to the Invoice and Post the Applied Deposit. This will Debit the Liability account and Credit Receivables.