Yes, the file counts. As one transaction, because there is only one charge to the customer's account.
I liken this to the Fed Staff's discussion about how to count transfers from a savings account to cover a DDA overdraft when there are multiple checks involved in the overdraft. The staff said that the answer depends on how the transfers from the savings account are made. If one transfer is generated at end of processing to cover the aggregate overdraft, it's counted as one transfer. If a transfer is created for each check that generates an overdraft, each transfer is counted separately.
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John S. Burnett
BankersOnline.com
Fighting for Compliance since 1976
Bankers' Threads User #8