It is necessary to file a DOEP on a Phase I exempt person other than banks and government entities. If the customer was originally a Phase II exempt person, it obviously is not a bank or a government entity.
Amending the exemption should be fine, but as there is no guidance on this you run the risk of being second guessed by a third party reviewer, albeit an auditor or an examiner. I would call the Helpline, memorialize their advice, then follow it.
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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.