I thnk you should check with counsel. However, a family trust can own a business, and it can operate under a tradestyle or fictitious name. Apparently, Doe obtained an EIN for the business since he has employees. If the business was a sole proprietorship, he could legitimately have given you either his SSN or the EIN for your records (although the IRS prefers the SSN route). It now appears that Doe has started a family trust and is moving his business and perhaps other assets into it. Again, that's a legitimate move, as far as I know.
If all is I have surmised, I see no reason you can't accept the trust's EIN for the business account, but make sure that the business shows on your records as the owner of the account.
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John S. Burnett
BankersOnline.com
Fighting for Compliance since 1976
Bankers' Threads User #8