If a customer no longer meets the definition of a Phase I exempt person then you would file the DOEP indicating it was a revocation. There is no provision in the regulation for "switching" an exemption from a Phase I to a Phase II. The LLC is a new customer and, under Phase II, you need a year's experience with the new customer to recognize them as an exempt person.
Nevertheless, I have heard anecdotal evidence from bankers that when they call FinCEN with this scenario they are told they can simply amend the exemption as long as the surviving customer meets Phase II requirements. I don't think that is technically correct, but when the Big Dog says it's okay, then you may conclude it's okay because the Big Dog says so.
Make your own call to FinCEN. If you are told that an amendment is acceptable document the phone call by writing a letter to the person you spoke with recapping your conversation. Your examiners and your auditors may want to see it.
From my perspective, you have a new customer and you start over.
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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.