Refile an already-filed return which is in progress with CRA is not allowed by CRA rules, not TurboTax. They will not disregard the original file to look into a newer one if both were sent electronically this is why they don't allow the second one to be sent unless the first one is finalized.
If you insist, you can mail a new return and wait for a longer process.
If both returns are prepared together, it means that the software had optimized the returns to interchanged expenses, deductions or split income between the returns. If one is filed, you cannot change the other. At this point, you have to start a new return if you want to change one of the returns.
