The salary advances are internal to the department. The Pay Centre has nothing to do with them. In my case, I wrote to Compensation, explained the problem, and showed them the calculations. They had to do some verification but within 5 days I had the deposit.

Since the advance isn't processed through the Pay Centre, the recovery is also not handled by the Pay Centre. In my case, a couple months after my pay file transferred, I received a polite email from our Salary Management folks asking me to either repay the entire amount or set up a payment plan. Easy peasy.

You do being up a good point: salary advances through the Pay Centre are almost guaranteed to eff you over at some point.