I am refiling my 2023 tax return because of an oversight. Do a pay my new balance owing now when I refile and wait to be reimbursed the difference from my first filing?

When I first filed, I paid my $600 owing. Now when refiling, I only owe $40. If I pay the $40 now, will be be reimbursed the $600 I previously paid?

After you file

Yes, the CRA will refund you any income tax overpayment, as long as you don't owe them money elsewhere ( GST/HST, benefits overpayments, amounts owing for prior years).