It doesn’t matter when the effective date changes on your profile, all that matters is that your effective CA date IS changed and reflects the correct date if CA bid award.
The way the pay system works is that the pay team in Phoenix (separate to ENY pay comp), simply looks at effective date and automatically back pays you the CA rate for the credit hours since that date.
Your pay comp auditor has absolutely Zero to do with your CA pay rates and back pay. It has all to do with the manager of crew coordination or whatever her title is, ensuring that department has sent the form to HR to change your effective CA date.