Making sure you have all the required documentation for a MIL/CTR. They could go to multiple branches and structure.
Also, 314(a) searches become an issue if you don't have a way to search all remitters.
Then there's the issue of if a non-customer loses the check and then you're stuck doing all the work for someone who's not even a customer of your bank.
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My opinions are my own, and not that of my employer.