Thanks, Ken. Our Deposit Ops manager did as you suggested, and most of the confusion was cleared up. She has since presented me with this information:
"We have experienced paying banks that have sent us the adjustment for not securing the physical check (which, of course you cannot with a mobile deposit). This accounts for most of the loss we’ve taken thus far. In this case, even under the new rules, since we took the mobile (no matter how it is endorsed) and we don’t have the physical check, we would take the loss. The new rules only speak to the ‘depositary bank that receives a deposit of an original paper check’ being indemnified against loss."
Is that accurate?
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Deep breath in...cleansing breath out...