The term "primary" has no meaning other than to indicate whose name is listed first in the title of a joint account.
Joe and Fred have a joint account. They each have individual accounts. Joe's individual account is overdrawn a lot. Fred's is not. Could you subject a check deposited to their joint account to a "repeated overdrafter" exception hold?
(d) Repeated overdrafts. If any account or combination of accounts of a depositary bank's customer has been repeatedly overdrawn, then for a period of six months after the last such overdraft, Secs. 229.10(c) and 229.12 do not apply to any of the accounts.
I don't see much ambiguity in the regulation; yes you could use the exception hold on the joint account. (That's consistent with the provisions of the large dollar exception hold that allow you to look at all of the customer's accounts, even those held in a different form of ownership.) Obviously, you're going to have to tell Fred about the basis for the hold.
If you have not been putting holds on Joe's deposits to his individual accounts it's going to look like you are just "outing" him to Fred. I would not do this unless it would appreciably reduce a risk I felt was significant...
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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.