While I don't know if I can actually provide you with sound advice, I had to reply, because your Subject header cracked me up. Anyone who uses the word "aberrant" is tops in my book. And I can just picture the situation you have described.
So here is what I think, and I have no legal basis for this, but it makes common sense to me. You should consult a healthcare attorney/accountant just to be sure:
1. As far as the ND moving in with her boyfriend and beginning to use a new last name, boyfriend or not, marriage or not, I would think there has to be a legal name change done on her part first. The new last name has to be recorded with the "powers that be" as required(SSA, IRS, DMV, etc). Once that is done, you can change her name with NPPES.
2. While a W-9 should be enough, I really don't know for sure...she should be able to keep her EIN/tax ID, and just submit the name change on it. After the name change is legal, of course.
Again, get her attorney and accountant involved in this, if necessary.