Anybody ever seen this: Error: THE_INVOICE_HAS_BEEN_SAVED_BUT_AUTOMATIC_APPLICATION_OF_THE_DEPOSIT_HAS_FAILED_PLEASE_APPLY_THE_DEPOSIT_MANUALLY

on what specific API are you encountering this error? I assume you are encountering this upon record.save() of the invoice record. Are you trying to link a deposit to the invoice within the script without a customer payment?

Yes it's on .save