If one account of customers' is overdrawn, can this exception hold reason be used on another account of the customer's that isn't overdrawn? I know new account holds look at the entire customer relationship, but repeated overdrafts doesn't, correct?

Certainly the exception applies to all of the customer's accounts.

229.13(d) (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. A depositary bank may consider a customer's account to be repeatedly overdrawn if--

(1) On six or more banking days within the preceding six months, the account balance is negative, or the account balance would have become negative if checks or other charges to the account had been paid; or

(2) On two or more banking days within the preceding six months, the account balance is negative, or the account balance would have become negative, in the amount of $5,525 [$6,725] or more, if checks or other charges to the account had been paid.

From section 229.13 - Exceptions

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. A depositary bank may consider a customer's account to be repeatedly overdrawn if--

(1) On six or more banking days within the preceding six months, the account balance is negative, or the account balance would have become negative if checks or other charges to the account had been paid; or

(2) On two or more banking days within the preceding six months, the account balance is negative, or the account balance would have become negative, in the amount of $5,525 [$6,725] or more, if checks or other charges to the account had been paid.

I would have directed you to 229.13(d), but I think the point has been driven home above.