The Milford portfolio manager at the centre of the FMA investigation was not a party to the settlement and is still facing enforcement action from the FMA.
Quirk said four of Milford's five business divisions had experienced "net in-flows" of funds, or had remained unchanged, since the settlement.
"Wholesale [clients] have different drivers of their decisions," he said. "We've got 20,000 retail clients and the vast majority of them have stayed with us."
Milford is also yet to reclaim a $281 million equities mandate that it previously held with the New Zealand Superannuation Fund.
That mandate was suspended in April as a result of the FMA investigation.
"We are taking time to consider the report in detail before deciding upon our response," a Super Fund spokeswoman said last month.
"We have the capacity to manage the funds in-house on an ongoing basis."