Receipt of a subpoena is a more than adequate catalyst for some enhanced due diligence. Keep in mind though, your customer may not be the object of the investigation.
If it's a grand jury subpoena you do not mention it in any SAR you might decide to file as the result of your investigation. Grand juries investigate suspected criminal activities and their actions are secret. If it's a garden variety subpoena follow the instructions to Part V in any SAR you decide to file:
k. Indicate whether there is any related litigation. If so, specify the names of the parties involved and the court where the action is pending.
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In this world you must be oh so smart or oh so pleasant. Well, for years I was smart. I recommend pleasant.